Difference between revisions of "RuntimeResourceClassification"

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The gCube Information System has recently extended in order to support a new type of Resource, the Runtime Resource. This Resource will bla bla
+
[[Category: Administrator's Guide]]
−
 
+
{| align="right"
 +
|| __TOC__
 +
|}
 
=== Runtime Resource Table ===
 
=== Runtime Resource Table ===
  
 
{| border="1" cellpadding="4" cellspacing="0"
 
{| border="1" cellpadding="4" cellspacing="0"
 
|-  
 
|-  
−
! style="background-color:#F2F2F2" width=150 | gCubeApp
+
! style="background-color:#F2F2F2" width=350 | gCubeApp
 
! style="background-color:#F2F2F2" width=200 | Component  
 
! style="background-color:#F2F2F2" width=200 | Component  
 
! style="background-color:#F2F2F2" width=200 | RuntimeResource   
 
! style="background-color:#F2F2F2" width=200 | RuntimeResource   
 
|-
 
|-
−
| pippo || puppa || [[#pappa|pappa]]
+
| Time Series / Ecological Modeling || GCubeGisViewer / Ecological Modeling suite || [[#Geo Server Runtime Resource|Geo Server]]
−
 
+
|-
 +
| Time Series / Ecological Modeling || GCubeGisViewer / Ecological Modeling suite || [[#Geo Network Runtime Resource|Geo Network]]
 +
|-
 +
| Time Series || Time Series Portlet || [[#RStudio Runtime Resource|RStudio]]
 +
|-
 +
| Time Series || Time Series Portlet  || [[#Time Series Database Runtime Resource|TimeSeries Database]]
 +
|-
 +
| Ecological Modeling || Ecological Modeling Service  || [[#Ecological Modeling Database Runtime Resource|Ecological Modeling Database]]
 +
|-
 +
| Ecological Modeling || Ecological Modeling Service  || [[#Gis Database Runtime Resource|Gis Database]]
 +
|-
 +
| Jackrabbit Repository || Home Library JCR  || [[#Jackrabbit Repository Runtime Resource|Jackrabbit Repository]]
 +
|-
 +
| Species Product Discovery || Obis plugin  || [[#Obis plugin Runtime Resource|Obis database]]
 +
|-
 +
| Species Product Discovery || BrazilianFlora plugin  || [[#BrazilianFlora plugin Runtime Resource|BrazilianFlora database]]
 +
|-
 +
| Species Product Discovery || CatalogueOfLife plugin  || [[#CatalogueOfLife plugin Runtime Resource|CatalogueOfLife Web Service]]
 +
|-
 +
| Species Product Discovery || ITIS plugin  || [[#ITIS plugin Runtime Resource|ITIS database]]
 +
|-
 +
| Species Product Discovery || SpeciesLink plugin  || [[#SpeciesLink plugin Runtime Resource|SpeciesLink Web Service]]
 +
|-
 +
| Species Product Discovery || WoRMS plugin  || [[#Worms plugin Runtime Resource|WoRMS Web Service]]
 +
|-
 +
| Species Product Discovery || NCBI plugin  || [[#NCBI plugin Runtime Resource|NCBI database]]
 +
|-
 +
| Species Product Discovery || IRMNG plugin  || [[#IRMNG plugin Runtime Resource|IRMNG database]]
 +
|-
 +
| Storage Manager Backend || Storage Manager  || [[#Storage Manager Runtime Resource|Storage manager backend]]
 +
|-
 +
| War Management Portlet || War Management Widget  || [[#Maven Repository Runtime Resource|Maven Repository]]
 
|}
 
|}
  
−
=== pappa ===
+
=== Geo Server Runtime Resource ===
 +
 
 +
The ''Geo Server Runtime Resource'' gives information about Geo Server instance deployed: where the Geo Server is deployed and what are the credentials to contact it.
 +
 
 +
==== Description====
 +
There will be one Runtime Resource for Geo Server instance.
 +
 
 +
The resource can be registered;
 +
* at VO level, if the Geo Server instance is shared between VREs.
 +
* at VRE level, if the Geo Server instance is VRE dedicated.
 +
 
 +
The Geo Server runtime resource is ''mandatory'' if in the VO/VRE are installed application using the GCube Gis Viewer widget.
 +
 
 +
==== Fields ====
 +
Other than required Runtime Resource fields almost one access point is necessary for a Geo Server Runtime Resource.
 +
 
 +
==== Ecological Modelling Configuration ====
 +
In order to let Ecological Modelling applications recognize the resource, its profile must be compliant with these rules :
 +
 
 +
* Category = ''Gis''
 +
* Platform/Name = ''GeoServer''
 +
 
 +
One AccessPoint is validated if :
 +
 
 +
* Endpoint EntryName =''geoserver''
 +
* Additional Properties :
 +
** aquamapsDefaultDistributionStyle (String)
 +
** aquamapsDataStore (String)
 +
** aquamapsWorkspace (String)
 +
 
 +
==== Example ====
 +
 
 +
<source lang="xml">
 +
  <Profile>
 +
      <Category>Gis</Category>
 +
      <Name>GeoServer</Name>
 +
      <Description>GeoServer configuration</Description>
 +
      <Platform>
 +
        <Name>GeoServer</Name>
 +
        <Version>2</Version>
 +
        <MinorVersion>1</MinorVersion>
 +
        <RevisionVersion>0</RevisionVersion>
 +
        <BuildVersion>0</BuildVersion>
 +
      </Platform>
 +
      <RunTime>
 +
        <HostedOn>geoserver-dev.d4science-ii.research-infrastructures.eu</HostedOn>
 +
        <GHN UniqueID="" />
 +
        <Status>READY</Status>
 +
      </RunTime>
 +
      <AccessPoint>
 +
        <Description>Main access point</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="geoserver">http://geoserver-dev.d4science-ii.research-infrastructures.eu/geoserver</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username>admin</Username>
 +
            <Password>**************</Password>
 +
        </AccessData>
 +
      </AccessPoint>
 +
  </Profile>
 +
</source>
 +
 
 +
=== Geo Network Runtime Resource ===
 +
 
 +
The ''Geo Network Runtime Resource'' gives information about Geo Network instance deployed: where the Geo Network is deployed and what are the credentials to contact it.
 +
 
 +
==== Description====
 +
There will be one Runtime Resource for each Geo Network instance.
 +
 
 +
The resource can be registered:
 +
* at VO level, if the Geo Network instance is shared between VREs.
 +
* at VRE level, if the Geo Network instance is VRE dedicated.
 +
 
 +
The Geo Network runtime resource is ''mandatory'' if in the VO/VRE are installed application using the GCube Gis Viewer widget.
 +
 
 +
==== Fields ====
 +
 
 +
The following Runtime Resource standard fields value are mandatory in order to discover it in the infrastructure :
 +
 
 +
* Category = ''Gis''
 +
* Platform/Name = ''geonetwork''
 +
 
 +
Other than required Runtime Resource fields almost one access point is needed with the following constraints :
 +
 
 +
* Endpoint EntryName = ''geonetwork''
 +
* boolean property ''master''
 +
* For each gCube scope (indicated as <SCOPE_NAME>) in which the Runtime Resource is registered, the access point should declare the following properties
 +
** encrypted string property <SCOPE_NAME>_Public containing the password of the public user for the given scope
 +
** encrypted string property <SCOPE_NAME>_Private containing the password of the private user for the given scope
 +
** integer property <SCOPE_NAME>_group containing the id of the publishing group for the given scope
 +
 
 +
==== Changes from gcube 4.0.0 ====
 +
 
 +
Mandatory fields remain the same of the previous version (we report here the defaults values released along with the library):
 +
* Category = ''Gis''
 +
* Platform/Name = ''geonetwork''
 +
* Endpoint EntryName = ''geonetwork''
 +
* boolean property ''master''
 +
 
 +
Also the AccessPoint credentials are expected to have administration rights on GeoNeotwork.
 +
 
 +
Scope configuration(s), if not found in the resource, is automatically generated and published at the first run of the library in a given scope.
 +
Please refer to [https://gcube.wiki.gcube-system.org/gcube/GeoNetwork_Configuration | GeoNetwork Configuration] for further information.
 +
 
 +
==== Example ====
 +
 
 +
<source lang="xml">
 +
  <Profile>
 +
      <Category>Gis</Category>
 +
      <Name>GeoNetwork</Name>
 +
      <Description>GeoNetwork configuration</Description>
 +
      <Platform>
 +
        <Name>geonetwork</Name>
 +
        <Version>2</Version>
 +
        <MinorVersion>6</MinorVersion>
 +
        <RevisionVersion>4</RevisionVersion>
 +
        <BuildVersion>0</BuildVersion>
 +
      </Platform>
 +
      <RunTime>
 +
        <HostedOn>geoserver-dev.d4science-ii.research-infrastructures.eu</HostedOn>
 +
        <GHN UniqueID="" />
 +
        <Status>READY</Status>
 +
      </RunTime>
 +
      <AccessPoint>
 +
        <Description>Main access point</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="geonetwork">http://geoserver-dev.d4science-ii.research-infrastructures.eu:8080/geonetwork</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username>admin</Username>
 +
            <Password>*********</Password>
 +
        </AccessData>
 +
      </AccessPoint>
 +
  </Profile>
 +
</source>
 +
 
 +
=== RStudio Runtime Resource ===
 +
 
 +
The ''RStudio Runtime Resource'' gives information about where the RStudio instance is deployed.
 +
 
 +
==== Description====
 +
The Runtime Resource should have "RStudio" name and there will be one Runtime Resource for RStudio instance.
 +
 
 +
The resource can be registered;
 +
* at VO level, if the RStudio instance is shared between VREs.
 +
* at VRE level, if the RStudio instance is VRE dedicated.
 +
 
 +
The RStudio runtime resource is ''mandatory'' if in the VO/VRE are installed application that offers access to RStudio instance.
 +
 
 +
==== Fields ====
 +
Other than required Runtime Resource fields almost one access point is necessary for a RStudio Runtime Resource with entry name "RStudio".
 +
 
 +
==== Example ====
 +
 
 +
<source lang="xml">
 +
  <Profile>
 +
      <Category>OnlineService</Category>
 +
      <Name>RStudio</Name>
 +
      <Description>RStudio™ is a free and open source integrated development environment (IDE) for R</Description>
 +
      <Platform>
 +
        <Name>RStudio</Name>
 +
        <Version>2</Version>
 +
        <MinorVersion>11</MinorVersion>
 +
        <RevisionVersion>1</RevisionVersion>
 +
        <BuildVersion>0</BuildVersion>
 +
      </Platform>
 +
      <RunTime>
 +
        <HostedOn>http://rstudio.research-infrastructures.eu</HostedOn>
 +
        <GHN UniqueID="" />
 +
        <Status>READY</Status>
 +
      </RunTime>
 +
      <AccessPoint>
 +
        <Description>RStudio</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="RStudio">http://rstudio.research-infrastructures.eu</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username />
 +
            <Password>6vW1u92cpdgHzYAgIurn9w==</Password>
 +
        </AccessData>
 +
      </AccessPoint>
 +
  </Profile>
 +
</source>
 +
 
 +
 
 +
=== Time Series Database Runtime Resource ===
 +
 
 +
The ''Time Series Database Runtime Resource'' gives information about where the Time Series Database is deployed.
 +
 
 +
==== Description====
 +
The Runtime Resource should have "TimeSeriesDatabase" name and there will be one Runtime Resource for Time Series instance.
 +
 
 +
The resource can be registered;
 +
* at VO level, if the Time Series instance is shared between VREs.
 +
* at VRE level, if the Time Series instance is VRE dedicated.
 +
 
 +
The Time Series runtime resource is ''mandatory'' if in the VO/VRE are installed application that want to access Time Series Database instance.
 +
 
 +
==== Fields ====
 +
Other than required Runtime Resource fields, two access point entry are required:
 +
* one with entry name "jdbc" with the necessary information for JDBC access to the database
 +
* one with entry name "readonly" with the readonly access information to the database
 +
Both the access point need a "dbname" property specifying the Time Series db name.
 +
 
 +
==== Example ====
 +
 
 +
<source lang="xml">
 +
  <Profile>
 +
      <Category>Database</Category>
 +
      <Name>TimeSeriesDatabase</Name>
 +
      <Description />
 +
      <Platform>
 +
        <Name>postgres</Name>
 +
        <Version>9</Version>
 +
        <MinorVersion>1</MinorVersion>
 +
        <RevisionVersion>0</RevisionVersion>
 +
        <BuildVersion>0</BuildVersion>
 +
      </Platform>
 +
      <RunTime>
 +
        <HostedOn>node24.d.d4science.research-infrastructures.eu</HostedOn>
 +
        <GHN UniqueID="" />
 +
        <Status>READY</Status>
 +
      </RunTime>
 +
      <AccessPoint>
 +
        <Description>jdbc conection url</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="jdbc">//node24.d.d4science.research-infrastructures.eu/timeseries</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username>gcube</Username>
 +
            <Password>*************</Password>
 +
        </AccessData>
 +
        <Properties>
 +
            <Property>
 +
              <Name>dbname</Name>
 +
              <Value encrypted="false">timeseries</Value>
 +
            </Property>
 +
        </Properties>
 +
      </AccessPoint>
 +
      <AccessPoint>
 +
        <Description>read only access point</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="readonly">//node24.d.d4science.research-infrastructures.eu/timeseries</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username>readonlyuser</Username>
 +
            <Password>************</Password>
 +
        </AccessData>
 +
        <Properties>
 +
            <Property>
 +
              <Name>dbname</Name>
 +
              <Value encrypted="false">timeseries</Value>
 +
            </Property>
 +
        </Properties>
 +
      </AccessPoint>
 +
  </Profile>
 +
</source>
 +
 
 +
=== Ecological Modelling Database Runtime Resource ===
 +
 
 +
The ''Ecological Modelling Database Runtime Resource'' gives information about access to the application database.
 +
 
 +
==== Description====
 +
 
 +
The resource can be registered;
 +
* at VO level, if the Time Series instance is shared between VREs.
 +
* at VRE level, if the Time Series instance is VRE dedicated.
 +
 
 +
The Ecological Modelling Database runtime resource is ''mandatory'' for each scopes in which an Ecological Modelling application instance is deployed.
 +
 
 +
==== Fields ====
 +
In order to be validated by the application, the Runtime Resource must follow these rules :
 +
 
 +
* Category = ''Database''
 +
* Platform/Name = ''postgres''
 +
 
 +
Two Access Points compliant with the following rules are required :
 +
 
 +
* Internal logic database access point :
 +
** Entry Name = ''jdbc''
 +
** user
 +
** password
 +
** Additional Properties :
 +
*** schema (String) = ''aquamaps''
 +
*** tableSpacePrefix (String)
 +
*** tableSpaceCount (Integer)
 +
*** maxConnection (Integer)
 +
 
 +
 
 +
* Publisher database access point :
 +
** Entry Name = ''jdbc''
 +
** user
 +
** password
 +
** Additional Properties :
 +
*** schema (String) = ''aquamapsPublisher''
 +
*** maxConnection (Integer)
 +
 
 +
==== Example ====
 +
 
 +
<source lang="xml">
 +
  <Profile>
 +
      <Category>Database</Category>
 +
      <Name>AquaMaps Service DataBase</Name>
 +
      <Description />
 +
      <Platform>
 +
        <Name>postgres</Name>
 +
        <Version>8</Version>
 +
        <MinorVersion>1</MinorVersion>
 +
        <RevisionVersion>1</RevisionVersion>
 +
        <BuildVersion>1</BuildVersion>
 +
      </Platform>
 +
      <RunTime>
 +
        <HostedOn>dbtest.research-infrastructures.eu</HostedOn>
 +
        <GHN UniqueID="0b473f00-fa6e-11e0-bb84-8d6426bd0941" />
 +
        <Status>READY</Status>
 +
      </RunTime>
 +
      <AccessPoint>
 +
        <Description>Internal buisness logic entry point</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="jdbc">//dbtest.research-infrastructures.eu:5432/aquamapsorgupdated</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username>utente</Username>
 +
            <Password>UwNMZOK7FlIjGPR+NZCV6w==</Password>
 +
        </AccessData>
 +
        <Properties>
 +
            <Property>
 +
              <Name>schema</Name>
 +
              <Value encrypted="false">aquamaps</Value>
 +
            </Property>
 +
            <Property>
 +
              <Name>maxConnection</Name>
 +
              <Value encrypted="false">20</Value>
 +
            </Property>
 +
            <Property>
 +
              <Name>tableSpaceCount</Name>
 +
              <Value encrypted="false">4</Value>
 +
            </Property>
 +
            <Property>
 +
              <Name>tableSpacePrefix</Name>
 +
              <Value encrypted="false">tbsp_</Value>
 +
            </Property>
 +
        </Properties>
 +
      </AccessPoint>
 +
      <AccessPoint>
 +
        <Description>publisher entry point</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="jdbc">//dbtest.research-infrastructures.eu:5432/apublisherdb</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username>utente</Username>
 +
            <Password>UwNMZOK7FlIjGPR+NZCV6w==</Password>
 +
        </AccessData>
 +
        <Properties>
 +
            <Property>
 +
              <Name>schema</Name>
 +
              <Value encrypted="false">aquamapsPublisher</Value>
 +
            </Property>
 +
            <Property>
 +
              <Name>maxConnection</Name>
 +
              <Value encrypted="false">20</Value>
 +
            </Property>
 +
        </Properties>
 +
      </AccessPoint>
 +
  </Profile>
 +
</source>
 +
 
 +
=== Gis Database Runtime Resource ===
 +
 
 +
The ''Gis Database Runtime Resource'' gives information about access to the GIS Database.
 +
 
 +
==== Description====
 +
 
 +
The resource can be registered;
 +
* at VO level, if the Time Series instance is shared between VREs.
 +
* at VRE level, if the Time Series instance is VRE dedicated.
 +
 
 +
The Gis Database Runtime Resource is ''mandatory'' for each scopes in which an Ecological Modelling application instance is deployed.
 +
 
 +
==== Fields ====
 +
 
 +
In order to be validated by the application, the Runtime Resource must follow these rules :
 +
 
 +
* Category = ''Database''
 +
* Platform/Name = ''postgis''
 +
 
 +
One Access Points compliant with the following rules is required :
 +
 
 +
* Internal logic database access point :
 +
** Entry Name = ''jdbc''
 +
** user
 +
** password
 +
** Additional Properties :
 +
*** aquamapsDataStore (Boolean) = ''true''
 +
*** aquamapsWorldTable (String)
 +
*** maxConnection (Integer)
 +
 
 +
==== Example ====
 +
 
 +
<source lang="xml">
 +
  <Profile>
 +
      <Category>Database</Category>
 +
      <Name>Geoserver database </Name>
 +
      <Description />
 +
      <Platform>
 +
        <Name>postgis</Name>
 +
        <Version>8</Version>
 +
        <MinorVersion>1</MinorVersion>
 +
        <RevisionVersion>1</RevisionVersion>
 +
        <BuildVersion>1</BuildVersion>
 +
      </Platform>
 +
      <RunTime>
 +
        <HostedOn>geoserver-dev.d4science-ii.research-infrastructures.eu</HostedOn>
 +
        <GHN UniqueID="" />
 +
        <Status>READY</Status>
 +
      </RunTime>
 +
      <AccessPoint>
 +
        <Description>aquamaps endpoint</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="jdbc">//geoserver-dev.d4science-ii.research-infrastructures.eu:5432/aquamapsdb</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username>postgres</Username>
 +
            <Password>HTGoibiGYhFhSlEf2xjKbg==</Password>
 +
        </AccessData>
 +
        <Properties>
 +
            <Property>
 +
              <Name>maxConnection</Name>
 +
              <Value encrypted="false">20</Value>
 +
            </Property>
 +
            <Property>
 +
              <Name>aquamapsWorldTable</Name>
 +
              <Value encrypted="false">world</Value>
 +
            </Property>
 +
            <Property>
 +
              <Name>aquamapsDataStore</Name>
 +
              <Value encrypted="false">true</Value>
 +
            </Property>
 +
        </Properties>
 +
      </AccessPoint>
 +
  </Profile>
 +
</source>
 +
 
 +
 
 +
=== Jackrabbit Repository Runtime Resource ===
 +
 
 +
The ''Jackrabbit Repository Runtime Resource'' gives information about access to the Jackrabbit repository.
 +
 
 +
==== Description====
 +
 
 +
The resource can be registered only at VO level
 +
 
 +
==== Fields ====
 +
 
 +
In order to be validated by the application, the Runtime Resource must follow these rules :
 +
 
 +
* Category = ''Database''
 +
* Platform/Name = ''JCR''
 +
 
 +
One Access Points compliant with the following rules is required :
 +
 
 +
* Internal logic repository access point :
 +
** Entry Name
 +
** user
 +
** password
 +
 
 +
 
 +
=== Obis plugin Runtime Resource ===
 +
 
 +
The ''Obis plugin Runtime Resource'' gives information about the Obis database instance: where the database is deployed and what are the credentials to contact it.
 +
 
 +
==== Description====
 +
There will be one Runtime Resource for database instance.
 +
 
 +
The resource can be registered;
 +
* at VO level, if the database instance is shared between VREs.
 +
* at VRE level, if the database instance is VRE dedicated.
 +
 
 +
The Obis plugin runtime resource is ''mandatory'' if in the VO/VRE is installed the Obis plugin.
 +
 
 +
==== Fields ====
 +
As for all the Species Product Discovery plugins the resource should have the same name of the plugin in this case '''Obis'''.
 +
Other than required Runtime Resource fields almost one access point is necessary for a Obis plugin Runtime Resource.
 +
The access point should have an endpoint with entryname =''jdbc'' with as value a JDBC connection url for the database instance.
 +
 
 +
==== Example ====
 +
 
 +
<source lang="xml">
 +
    <Profile>
 +
      <Category>BiodiversityRepository</Category>
 +
      <Name>Obis</Name>
 +
      <Description>Obis database coordinates</Description>
 +
      <Platform>
 +
        <Name>Postgresql</Name>
 +
        <Version>8</Version>
 +
        <MinorVersion>4</MinorVersion>
 +
        <RevisionVersion>0</RevisionVersion>
 +
        <BuildVersion>0</BuildVersion>
 +
      </Platform>
 +
      <RunTime>
 +
        <HostedOn>geoserver2.i-marine.research-infrastructures.eu</HostedOn>
 +
        <GHN UniqueID="" />
 +
        <Status>READY</Status>
 +
      </RunTime>
 +
      <AccessPoint>
 +
        <Description>jdbc access point</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="jdbc">jdbc:postgresql://geoserver2.i-marine.research-infrastructures.eu/obis</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username>postgres</Username>
 +
            <Password>***********</Password>
 +
        </AccessData>
 +
      </AccessPoint>
 +
  </Profile>
 +
</source>
 +
 
 +
 
 +
 
 +
=== BrazilianFlora plugin Runtime Resource ===
 +
 
 +
The ''BrazilianFlora plugin Runtime Resource'' gives the link to FloraBrasil API and the credentials to contact BrazilianFlora database.
 +
 
 +
==== Description====
 +
Since FloraBrasil API permits to retrieve taxa using just the exact name, specifying its rank, we create a database by Lista de Espécies da Flora do Brasil through FloraBrasil API, which we are using to populate the BrazilianFlora database.
 +
 
 +
==== Fields ====
 +
We have 2 Access Points, with EntryName:
 +
* "rest": it contains the FloraBrasil API link.
 +
* "jdbc": it contains the information for JDBC access to the postgres database with Username and Password.
 +
 
 +
==== Example ====
 +
 
 +
<source lang="xml">
 +
    <Profile>     
 +
      <Category>BiodiversityRepository</Category>   
 +
      <Name>BrazilianFlora</Name>       
 +
      <Description>RuntimeResource for  BrazilianFlora repository</Description>       
 +
      <Platform>           
 +
        <Name>Web Service</Name>           
 +
        <Version>1</Version>           
 +
        <MinorVersion>0</MinorVersion>           
 +
        <RevisionVersion>0</RevisionVersion>           
 +
        <BuildVersion>0</BuildVersion>     
 +
      </Platform>   
 +
      <RunTime>         
 +
        <HostedOn>node24.d.d4science.research-infrastructures.eu</HostedOn>         
 +
        <GHN UniqueID="" />           
 +
        <Status>READY</Status>       
 +
      </RunTime>   
 +
    <AccessPoint>   
 +
        <Description>rest service access point</Description>         
 +
        <Interface>               
 +
            <Endpoint EntryName="rest">http://checklist.florabrasil.net/service/</Endpoint>           
 +
        </Interface>           
 +
        <AccessData>               
 +
            <Username />               
 +
            <Password></Password>           
 +
        </AccessData>       
 +
      </AccessPoint>   
 +
      <AccessPoint>           
 +
        <Description>postgres</Description>           
 +
        <Interface>               
 +
            <Endpoint EntryName="jdbc">jdbc:postgresql://node24.d.d4science.research-infrastructures.eu/brazilianFlora</Endpoint>           
 +
        </Interface>       
 +
        <AccessData>               
 +
            <Username>gcube</Username>             
 +
            <Password>***********</Password>   
 +
        </AccessData>       
 +
        <Properties>       
 +
            <Property>                 
 +
              <Name>hostName</Name>                 
 +
              <Value encrypted="false">node24.d.d4science.research-infrastructures.eu</Value>           
 +
            </Property>         
 +
        </Properties>     
 +
      </AccessPoint> 
 +
  </Profile>
 +
</source>
 +
 
 +
=== CatalogueOfLife plugin Runtime Resource ===
 +
 
 +
The ''CatalogueOfLife plugin Runtime Resource'' gives the link to CatalogueOfLife web service which provide programmatic access to the checklist.
 +
 
 +
==== Description====
 +
For a programmatic access to the CatalogueOfLife Web service we use the Annual Checklist web service available. Using a correctly formatted URL we receive an XML document containing the taxonomic information we require.
 +
 
 +
==== Fields ====
 +
CatalogueOfLife plugin Runtime Resource has a access point and its endpoint has entryname ''CatalogueOfLife''. Its value is a link to CatalogueOfLife web service.
 +
 
 +
 
 +
 
 +
=== ITIS plugin Runtime Resource ===
 +
 
 +
The ''ITIS plugin Runtime Resource'' gives the link to ITIS database dump files.
 +
 
 +
==== Description====
 +
For a programmatic access to ITIS, the Integrated Taxonomic Information System, we download and extract the file on the system we use to load the MySQL database.
 +
 
 +
==== Fields ====
 +
An access point entry, with entry name "jdbc", is required. It contains the information for JDBC access to the database.
 +
ITIS plugin Runtime Resource has a access point and its endpoint.
 +
 
 +
==== Example ====
 +
 
 +
<source lang="xml">
 +
    <Profile>     
 +
      <Category>BiodiversityRepository</Category>   
 +
      <Name>ITIS</Name>     
 +
      <Description>RuntimeResource for ITIS Plugin</Description> 
 +
      <Platform>           
 +
        <Name>MySQL</Name>           
 +
        <Version>5</Version>         
 +
        <MinorVersion>1</MinorVersion>         
 +
        <RevisionVersion>62</RevisionVersion>       
 +
        <BuildVersion>0</BuildVersion>     
 +
      </Platform>   
 +
      <RunTime>         
 +
        <HostedOn>node24.d.d4science.research-infrastructures.eu</HostedOn>         
 +
        <GHN UniqueID="" />           
 +
        <Status>READY</Status>       
 +
      </RunTime>       
 +
      <AccessPoint>           
 +
        <Description>jdbc connection</Description>           
 +
        <Interface>               
 +
            <Endpoint EntryName="jdbc">jdbc:mysql://node24.d.d4science.research-infrastructures.eu/ITIS</Endpoint>           
 +
        </Interface>       
 +
        <AccessData>               
 +
            <Username>itisuser</Username>             
 +
            <Password>***********</Password>   
 +
        </AccessData>       
 +
        <Properties>       
 +
            <Property>                 
 +
              <Name>hostName</Name>                 
 +
              <Value encrypted="false">node24.d.d4science.research-infrastructures.eu</Value>           
 +
            </Property>         
 +
        </Properties>     
 +
      </AccessPoint> 
 +
  </Profile>
 +
</source>
 +
 
 +
=== SpeciesLink plugin Runtime Resource ===
 +
 
 +
The '' SpeciesLink plugin Runtime Resource'' gives the link to SpeciesLink web service which provide programmatic access to data.
 +
 
 +
==== Description====
 +
SpeciesLink plugin data is accessible through programmatic search on a web service interface based on the TAPIR protocol and on the DarwinCore data standard.
 +
 
 +
==== Fields ====
 +
One access point is necessary for a SpeciesLink plugin Runtime Resource.
 +
* EntryName = ''tapir''
 +
* Additional Properties:
 +
** model
 +
The property ''model'' contains the output model definition, in this case the DarwinCore data standard.
 +
 
 +
==== Example ====
 +
 
 +
<source lang="xml">
 +
    <Profile>   
 +
      <Category>BiodiversityRepository</Category>     
 +
      <Name>SpeciesLink</Name>     
 +
      <Description>RuntimeResource for SpeciesLink repository</Description>       
 +
      <Platform>         
 +
        <Name>TapirLink</Name>         
 +
        <Version>0</Version>         
 +
        <MinorVersion>7</MinorVersion>           
 +
        <RevisionVersion>1</RevisionVersion>         
 +
        <BuildVersion>0</BuildVersion>     
 +
      </Platform>     
 +
      <RunTime>           
 +
        <HostedOn>tapir.cria.org.br</HostedOn>           
 +
        <GHN UniqueID="" />           
 +
        <Status>READY</Status>     
 +
      </RunTime>       
 +
      <AccessPoint>         
 +
        <Description>tapir protocol access point</Description>         
 +
        <Interface>               
 +
            <Endpoint EntryName="tapir">http://tapir.cria.org.br/tapirlink/tapir.php/specieslink</Endpoint>           
 +
        </Interface>           
 +
        <AccessData>               
 +
            <Username />             
 +
            <Password>***********</Password>           
 +
        </AccessData>         
 +
        <Properties>             
 +
            <Property>           
 +
              <Name>model</Name>                 
 +
              <Value encrypted="false">http://rs.tdwg.org/tapir/cs/dwc/1.4/model/dw_core_geo_cur.xml</Value>             
 +
            </Property>         
 +
        </Properties>     
 +
      </AccessPoint> 
 +
  </Profile>
 +
</source>
 +
 
 +
 
 +
=== Worms plugin Runtime Resource ===
 +
 
 +
The '' WoRMS plugin Runtime Resource'' gives the link to the WoRMS webservice to feed our application with standard WoRMS taxonomy.
 +
 
 +
==== Description====
 +
WoRMS webservice currently supports the platform-independent SOAP/WSDL standard. The webservice exposes a standard taxonomy of marine animal species integrated with Global Species Databases (GSD).
 +
 
 +
==== Fields ====
 +
Worms plugin Runtime Resource has an access point and its endpoint has entryname ''Worms''. Its value is a link to Worms web service.
 +
 
 +
 
 +
=== NCBI plugin Runtime Resource ===
 +
 
 +
The ''NCBI plugin Runtime Resource'' gives the link to NCBI database dump files.
 +
 
 +
==== Description====
 +
For a programmatic access to NCBI, the National Center for Biotechnology Information, we download and extract the file on the system we use to load the PostgreSQL database.
 +
 
 +
==== Fields ====
 +
NCBI plugin Runtime Resource has 2 Access Points, with EntryName:
 +
* "ftp": it contains the ftp link to database dump.
 +
* "jdbc": it contains the information for JDBC access to the postgres database with Username and Password.
 +
 
 +
 
 +
=== IRMNG plugin Runtime Resource ===
 +
 
 +
The ''IRMNG plugin Runtime Resource'' gives the link to IRMNG database dump files in Darwin Core Archive.
 +
 
 +
==== Description====
 +
For a programmatic access to IRMNG, the Interim Register of Marine and Nonmarine Genera, we download and extract the file on the system we use to load the PostgreSQL database.
 +
 
 +
==== Fields ====
 +
IRMNG plugin Runtime Resource has 2 Access Points, with EntryName:
 +
* "dump": it contains the link to database dump.
 +
* "jdbc": it contains the information for JDBC access to the postgres database with Username and Password.
 +
 
 +
 
 +
=== Storage Manager Runtime Resource ===
 +
 
 +
The ''Storage Manager Runtime Resource'' gives information about servers backend of storageManager library.
 +
 
 +
==== Description====
 +
 
 +
The servers are used to store file by storageManager library. The server descripted can be a only one server or a cluster of server.
 +
The runtime resource define the type of the server and the ip address. The resource is registered at VO level
 +
 
 +
==== Fields ====
 +
 
 +
In order to be validated by the application, the Runtime Resource must follow these rules :
 +
 
 +
* Category = ''DataStorage''
 +
* Name= ''StorageManager
 +
* Platform/Name = ''storage-manager''
 +
 
 +
One Access Points compliant with the following rules is required :
 +
 
 +
* Internal logic repository access point :
 +
** Entry Name: ''server[i]'' where i is an integer. This field contains the ip address of the server
 +
** property ''host'' that define the host name of the server
 +
** property ''type'' that define the type of the backend, in this case a MongoDB server
 +
 
 +
==== Example ====
 +
 
 +
<source lang="xml">
 +
<Resource version="0.4.x">
 +
  <ID>0717b450-a698-11e2-900a-a46c6ff57f05</ID>
 +
  <Type>RuntimeResource</Type>
 +
  <Scopes>
 +
      <Scope>/d4science.research-infrastructures.eu</Scope>
 +
      <Scope>/d4science.research-infrastructures.eu/Ecosystem</Scope>
 +
  </Scopes>
 +
  <Profile>
 +
      <Category>DataStorage</Category>
 +
      <Name>StorageManager</Name>
 +
      <Description>Backend definition  for StorageManager library</Description>
 +
      <Platform>
 +
        <Name>storage-manager</Name>
 +
        <Version>2</Version>
 +
        <MinorVersion>0</MinorVersion>
 +
        <RevisionVersion>0</RevisionVersion>
 +
        <BuildVersion>0</BuildVersion>
 +
      </Platform>
 +
      <RunTime>
 +
        <HostedOn>d4science.org</HostedOn>
 +
        <GHN UniqueID="" />
 +
        <Status>READY</Status>
 +
      </RunTime>
 +
      <AccessPoint>
 +
        <Description>MongoDB server</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="server1">146.48.122.138</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username />
 +
            <Password>6vW1u92cpdgHzYAgIurn9w==</Password>
 +
        </AccessData>
 +
        <Properties>
 +
            <Property>
 +
              <Name>host</Name>
 +
              <Value encrypted="false">node58.p.d4science.research-infrastructures.eu</Value>
 +
            </Property>
 +
            <Property>
 +
              <Name>type</Name>
 +
              <Value encrypted="false">MongoDB</Value>
 +
            </Property>
 +
        </Properties>
 +
      </AccessPoint>
 +
      <AccessPoint>
 +
        <Description>MongoDB server</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="server2">146.48.122.153</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username />
 +
            <Password>6vW1u92cpdgHzYAgIurn9w==</Password>
 +
        </AccessData>
 +
        <Properties>
 +
            <Property>
 +
              <Name>host</Name>
 +
              <Value encrypted="false">node67.p.d4science.research-infrastructures.eu</Value>
 +
            </Property>
 +
            <Property>
 +
              <Name>type</Name>
 +
              <Value encrypted="false">MongoDB</Value>
 +
            </Property>
 +
        </Properties>
 +
      </AccessPoint>
 +
      <AccessPoint>
 +
        <Description>MongoDB server</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="server3">146.48.122.102</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username />
 +
            <Password>6vW1u92cpdgHzYAgIurn9w==</Password>
 +
        </AccessData>
 +
        <Properties>
 +
            <Property>
 +
              <Name>host</Name>
 +
              <Value encrypted="false">node80.p.d4science.research-infrastructures.eu</Value>
 +
            </Property>
 +
            <Property>
 +
              <Name>type</Name>
 +
              <Value encrypted="false">MongoDB</Value>
 +
            </Property>
 +
        </Properties>
 +
      </AccessPoint>
 +
  </Profile>
 +
</Resource>
 +
</source>
 +
 
 +
=== Maven Repository Runtime Resource ===
 +
 
 +
The ''Maven Repository Runtime Resource'' gives information about a Maven Repository instance providing this info:
 +
* Host where the repository is deployed (mandatory)
 +
* Endpoints
 +
** Maven repo endpoint (mandatory)
 +
** Other endpoints (like the nexus browser url)
 +
 
 +
==== Description====
 +
There will be one Runtime Resource for each repository instance.
 +
 
 +
The resource can be registered;
 +
* at ROOT level, if the repository instance is shared for the entire infrastructure.
 +
* at VO level, if the repository instance is shared between VREs.
 +
* at VRE level, if the repository instance is VRE dedicated.
 +
 
 +
The Maven Repository runtime resource is ''mandatory'' if in the Infrastructure/VO/VRE is installed:
 +
* War Management Portlet
 +
* Software Upload Wizard Portlet
 +
 
 +
==== Fields ====
 +
The Runtime Resource must have:
 +
* Category: ''Maven''
 +
* Name: ''MavenRepository''
 +
* Runtime tag filled with data regarding the host where the repository is hosted.
 +
* An access point pointing to the root repository URL with these characteristics:
 +
** Endpoint with entryname ''RepositoryUrl'' with a repository url as value (e.g.: http://maven.research-infrastructures.eu:8081/nexus/content/repositories/gcube-snapshots/);
 +
** A property with name ''repositoryId'' that specify the repository id (e.g.: gcube-snapshots).
 +
 
 +
==== Example ====
 +
 
 +
<source lang="xml">
 +
  <Profile>
 +
      <Category>Maven</Category>
 +
      <Name>MavenRepository</Name>
 +
      <Description>Maven Repository information</Description>
 +
      <Platform>
 +
        <Name>Nexus</Name>
 +
        <Version>1</Version>
 +
        <MinorVersion>0</MinorVersion>
 +
        <RevisionVersion>0</RevisionVersion>
 +
        <BuildVersion>0</BuildVersion>
 +
      </Platform>
 +
      <RunTime>
 +
        <HostedOn>maven.research-infrastructures.eu</HostedOn>
 +
        <GHN UniqueID="" />
 +
        <Status>READY</Status>
 +
      </RunTime>
 +
      <AccessPoint>
 +
        <Description>RepositoryUrl</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="RepositoryUrl">http://maven.research-infrastructures.eu:8081/nexus/content/repositories/gcube-snapshots/</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username />
 +
            <Password>*************</Password>
 +
        </AccessData>
 +
        <Properties>
 +
            <Property>
 +
              <Name>repositoryId</Name>
 +
              <Value encrypted="false">gcube-snapshots</Value>
 +
            </Property>
 +
        </Properties>
 +
      </AccessPoint>
 +
      <AccessPoint>
 +
        <Description>Nexus Browser Url</Description>
 +
        <Interface>
 +
            <Endpoint EntryName="NexusUrl">http://maven.research-infrastructures.eu/nexus/index.html#view-repositories;gcube-snapshots~browsestorage</Endpoint>
 +
        </Interface>
 +
        <AccessData>
 +
            <Username />
 +
            <Password>**************</Password>
 +
        </AccessData>
 +
      </AccessPoint>
 +
  </Profile>
 +
</source>

Latest revision as of 15:00, 23 May 2016

Runtime Resource Table

gCubeApp Component RuntimeResource
Time Series / Ecological Modeling GCubeGisViewer / Ecological Modeling suite Geo Server
Time Series / Ecological Modeling GCubeGisViewer / Ecological Modeling suite Geo Network
Time Series Time Series Portlet RStudio
Time Series Time Series Portlet TimeSeries Database
Ecological Modeling Ecological Modeling Service Ecological Modeling Database
Ecological Modeling Ecological Modeling Service Gis Database
Jackrabbit Repository Home Library JCR Jackrabbit Repository
Species Product Discovery Obis plugin Obis database
Species Product Discovery BrazilianFlora plugin BrazilianFlora database
Species Product Discovery CatalogueOfLife plugin CatalogueOfLife Web Service
Species Product Discovery ITIS plugin ITIS database
Species Product Discovery SpeciesLink plugin SpeciesLink Web Service
Species Product Discovery WoRMS plugin WoRMS Web Service
Species Product Discovery NCBI plugin NCBI database
Species Product Discovery IRMNG plugin IRMNG database
Storage Manager Backend Storage Manager Storage manager backend
War Management Portlet War Management Widget Maven Repository

Geo Server Runtime Resource

The Geo Server Runtime Resource gives information about Geo Server instance deployed: where the Geo Server is deployed and what are the credentials to contact it.

Description

There will be one Runtime Resource for Geo Server instance.

The resource can be registered;

  • at VO level, if the Geo Server instance is shared between VREs.
  • at VRE level, if the Geo Server instance is VRE dedicated.

The Geo Server runtime resource is mandatory if in the VO/VRE are installed application using the GCube Gis Viewer widget.

Fields

Other than required Runtime Resource fields almost one access point is necessary for a Geo Server Runtime Resource.

Ecological Modelling Configuration

In order to let Ecological Modelling applications recognize the resource, its profile must be compliant with these rules :

  • Category = Gis
  • Platform/Name = GeoServer

One AccessPoint is validated if :

  • Endpoint EntryName =geoserver
  • Additional Properties :
    • aquamapsDefaultDistributionStyle (String)
    • aquamapsDataStore (String)
    • aquamapsWorkspace (String)

Example

  <Profile>
      <Category>Gis</Category>
      <Name>GeoServer</Name>
      <Description>GeoServer configuration</Description>
      <Platform>
         <Name>GeoServer</Name>
         <Version>2</Version>
         <MinorVersion>1</MinorVersion>
         <RevisionVersion>0</RevisionVersion>
         <BuildVersion>0</BuildVersion>
      </Platform>
      <RunTime>
         <HostedOn>geoserver-dev.d4science-ii.research-infrastructures.eu</HostedOn>
         <GHN UniqueID="" />
         <Status>READY</Status>
      </RunTime>
      <AccessPoint>
         <Description>Main access point</Description>
         <Interface>
            <Endpoint EntryName="geoserver">http://geoserver-dev.d4science-ii.research-infrastructures.eu/geoserver</Endpoint>
         </Interface>
         <AccessData>
            <Username>admin</Username>
            <Password>**************</Password>
         </AccessData>
      </AccessPoint>
   </Profile>

Geo Network Runtime Resource

The Geo Network Runtime Resource gives information about Geo Network instance deployed: where the Geo Network is deployed and what are the credentials to contact it.

Description

There will be one Runtime Resource for each Geo Network instance.

The resource can be registered:

  • at VO level, if the Geo Network instance is shared between VREs.
  • at VRE level, if the Geo Network instance is VRE dedicated.

The Geo Network runtime resource is mandatory if in the VO/VRE are installed application using the GCube Gis Viewer widget.

Fields

The following Runtime Resource standard fields value are mandatory in order to discover it in the infrastructure :

  • Category = Gis
  • Platform/Name = geonetwork

Other than required Runtime Resource fields almost one access point is needed with the following constraints :

  • Endpoint EntryName = geonetwork
  • boolean property master
  • For each gCube scope (indicated as <SCOPE_NAME>) in which the Runtime Resource is registered, the access point should declare the following properties
    • encrypted string property <SCOPE_NAME>_Public containing the password of the public user for the given scope
    • encrypted string property <SCOPE_NAME>_Private containing the password of the private user for the given scope
    • integer property <SCOPE_NAME>_group containing the id of the publishing group for the given scope

Changes from gcube 4.0.0

Mandatory fields remain the same of the previous version (we report here the defaults values released along with the library):

  • Category = Gis
  • Platform/Name = geonetwork
  • Endpoint EntryName = geonetwork
  • boolean property master

Also the AccessPoint credentials are expected to have administration rights on GeoNeotwork.

Scope configuration(s), if not found in the resource, is automatically generated and published at the first run of the library in a given scope. Please refer to | GeoNetwork Configuration for further information.

Example

  <Profile>
      <Category>Gis</Category>
      <Name>GeoNetwork</Name>
      <Description>GeoNetwork configuration</Description>
      <Platform>
         <Name>geonetwork</Name>
         <Version>2</Version>
         <MinorVersion>6</MinorVersion>
         <RevisionVersion>4</RevisionVersion>
         <BuildVersion>0</BuildVersion>
      </Platform>
      <RunTime>
         <HostedOn>geoserver-dev.d4science-ii.research-infrastructures.eu</HostedOn>
         <GHN UniqueID="" />
         <Status>READY</Status>
      </RunTime>
      <AccessPoint>
         <Description>Main access point</Description>
         <Interface>
            <Endpoint EntryName="geonetwork">http://geoserver-dev.d4science-ii.research-infrastructures.eu:8080/geonetwork</Endpoint>
         </Interface>
         <AccessData>
            <Username>admin</Username>
            <Password>*********</Password>
         </AccessData>
      </AccessPoint>
   </Profile>

RStudio Runtime Resource

The RStudio Runtime Resource gives information about where the RStudio instance is deployed.

Description

The Runtime Resource should have "RStudio" name and there will be one Runtime Resource for RStudio instance.

The resource can be registered;

  • at VO level, if the RStudio instance is shared between VREs.
  • at VRE level, if the RStudio instance is VRE dedicated.

The RStudio runtime resource is mandatory if in the VO/VRE are installed application that offers access to RStudio instance.

Fields

Other than required Runtime Resource fields almost one access point is necessary for a RStudio Runtime Resource with entry name "RStudio".

Example

  <Profile>
      <Category>OnlineService</Category>
      <Name>RStudio</Name>
      <Description>RStudio™ is a free and open source integrated development environment (IDE) for R</Description>
      <Platform>
         <Name>RStudio</Name>
         <Version>2</Version>
         <MinorVersion>11</MinorVersion>
         <RevisionVersion>1</RevisionVersion>
         <BuildVersion>0</BuildVersion>
      </Platform>
      <RunTime>
         <HostedOn>http://rstudio.research-infrastructures.eu</HostedOn>
         <GHN UniqueID="" />
         <Status>READY</Status>
      </RunTime>
      <AccessPoint>
         <Description>RStudio</Description>
         <Interface>
            <Endpoint EntryName="RStudio">http://rstudio.research-infrastructures.eu</Endpoint>
         </Interface>
         <AccessData>
            <Username />
            <Password>6vW1u92cpdgHzYAgIurn9w==</Password>
         </AccessData>
      </AccessPoint>
   </Profile>


Time Series Database Runtime Resource

The Time Series Database Runtime Resource gives information about where the Time Series Database is deployed.

Description

The Runtime Resource should have "TimeSeriesDatabase" name and there will be one Runtime Resource for Time Series instance.

The resource can be registered;

  • at VO level, if the Time Series instance is shared between VREs.
  • at VRE level, if the Time Series instance is VRE dedicated.

The Time Series runtime resource is mandatory if in the VO/VRE are installed application that want to access Time Series Database instance.

Fields

Other than required Runtime Resource fields, two access point entry are required:

  • one with entry name "jdbc" with the necessary information for JDBC access to the database
  • one with entry name "readonly" with the readonly access information to the database

Both the access point need a "dbname" property specifying the Time Series db name.

Example

  <Profile>
      <Category>Database</Category>
      <Name>TimeSeriesDatabase</Name>
      <Description />
      <Platform>
         <Name>postgres</Name>
         <Version>9</Version>
         <MinorVersion>1</MinorVersion>
         <RevisionVersion>0</RevisionVersion>
         <BuildVersion>0</BuildVersion>
      </Platform>
      <RunTime>
         <HostedOn>node24.d.d4science.research-infrastructures.eu</HostedOn>
         <GHN UniqueID="" />
         <Status>READY</Status>
      </RunTime>
      <AccessPoint>
         <Description>jdbc conection url</Description>
         <Interface>
            <Endpoint EntryName="jdbc">//node24.d.d4science.research-infrastructures.eu/timeseries</Endpoint>
         </Interface>
         <AccessData>
            <Username>gcube</Username>
            <Password>*************</Password>
         </AccessData>
         <Properties>
            <Property>
               <Name>dbname</Name>
               <Value encrypted="false">timeseries</Value>
            </Property>
         </Properties>
      </AccessPoint>
      <AccessPoint>
         <Description>read only access point</Description>
         <Interface>
            <Endpoint EntryName="readonly">//node24.d.d4science.research-infrastructures.eu/timeseries</Endpoint>
         </Interface>
         <AccessData>
            <Username>readonlyuser</Username>
            <Password>************</Password>
         </AccessData>
         <Properties>
            <Property>
               <Name>dbname</Name>
               <Value encrypted="false">timeseries</Value>
            </Property>
         </Properties>
      </AccessPoint>
   </Profile>

Ecological Modelling Database Runtime Resource

The Ecological Modelling Database Runtime Resource gives information about access to the application database.

Description

The resource can be registered;

  • at VO level, if the Time Series instance is shared between VREs.
  • at VRE level, if the Time Series instance is VRE dedicated.

The Ecological Modelling Database runtime resource is mandatory for each scopes in which an Ecological Modelling application instance is deployed.

Fields

In order to be validated by the application, the Runtime Resource must follow these rules :

  • Category = Database
  • Platform/Name = postgres

Two Access Points compliant with the following rules are required :

  • Internal logic database access point :
    • Entry Name = jdbc
    • user
    • password
    • Additional Properties :
      • schema (String) = aquamaps
      • tableSpacePrefix (String)
      • tableSpaceCount (Integer)
      • maxConnection (Integer)


  • Publisher database access point :
    • Entry Name = jdbc
    • user
    • password
    • Additional Properties :
      • schema (String) = aquamapsPublisher
      • maxConnection (Integer)

Example

  <Profile>
      <Category>Database</Category>
      <Name>AquaMaps Service DataBase</Name>
      <Description />
      <Platform>
         <Name>postgres</Name>
         <Version>8</Version>
         <MinorVersion>1</MinorVersion>
         <RevisionVersion>1</RevisionVersion>
         <BuildVersion>1</BuildVersion>
      </Platform>
      <RunTime>
         <HostedOn>dbtest.research-infrastructures.eu</HostedOn>
         <GHN UniqueID="0b473f00-fa6e-11e0-bb84-8d6426bd0941" />
         <Status>READY</Status>
      </RunTime>
      <AccessPoint>
         <Description>Internal buisness logic entry point</Description>
         <Interface>
            <Endpoint EntryName="jdbc">//dbtest.research-infrastructures.eu:5432/aquamapsorgupdated</Endpoint>
         </Interface>
         <AccessData>
            <Username>utente</Username>
            <Password>UwNMZOK7FlIjGPR+NZCV6w==</Password>
         </AccessData>
         <Properties>
            <Property>
               <Name>schema</Name>
               <Value encrypted="false">aquamaps</Value>
            </Property>
            <Property>
               <Name>maxConnection</Name>
               <Value encrypted="false">20</Value>
            </Property>
            <Property>
               <Name>tableSpaceCount</Name>
               <Value encrypted="false">4</Value>
            </Property>
            <Property>
               <Name>tableSpacePrefix</Name>
               <Value encrypted="false">tbsp_</Value>
            </Property>
         </Properties>
      </AccessPoint>
      <AccessPoint>
         <Description>publisher entry point</Description>
         <Interface>
            <Endpoint EntryName="jdbc">//dbtest.research-infrastructures.eu:5432/apublisherdb</Endpoint>
         </Interface>
         <AccessData>
            <Username>utente</Username>
            <Password>UwNMZOK7FlIjGPR+NZCV6w==</Password>
         </AccessData>
         <Properties>
            <Property>
               <Name>schema</Name>
               <Value encrypted="false">aquamapsPublisher</Value>
            </Property>
            <Property>
               <Name>maxConnection</Name>
               <Value encrypted="false">20</Value>
            </Property>
         </Properties>
      </AccessPoint>
   </Profile>

Gis Database Runtime Resource

The Gis Database Runtime Resource gives information about access to the GIS Database.

Description

The resource can be registered;

  • at VO level, if the Time Series instance is shared between VREs.
  • at VRE level, if the Time Series instance is VRE dedicated.

The Gis Database Runtime Resource is mandatory for each scopes in which an Ecological Modelling application instance is deployed.

Fields

In order to be validated by the application, the Runtime Resource must follow these rules :

  • Category = Database
  • Platform/Name = postgis

One Access Points compliant with the following rules is required :

  • Internal logic database access point :
    • Entry Name = jdbc
    • user
    • password
    • Additional Properties :
      • aquamapsDataStore (Boolean) = true
      • aquamapsWorldTable (String)
      • maxConnection (Integer)

Example

  <Profile>
      <Category>Database</Category>
      <Name>Geoserver database </Name>
      <Description />
      <Platform>
         <Name>postgis</Name>
         <Version>8</Version>
         <MinorVersion>1</MinorVersion>
         <RevisionVersion>1</RevisionVersion>
         <BuildVersion>1</BuildVersion>
      </Platform>
      <RunTime>
         <HostedOn>geoserver-dev.d4science-ii.research-infrastructures.eu</HostedOn>
         <GHN UniqueID="" />
         <Status>READY</Status>
      </RunTime>
      <AccessPoint>
         <Description>aquamaps endpoint</Description>
         <Interface>
            <Endpoint EntryName="jdbc">//geoserver-dev.d4science-ii.research-infrastructures.eu:5432/aquamapsdb</Endpoint>
         </Interface>
         <AccessData>
            <Username>postgres</Username>
            <Password>HTGoibiGYhFhSlEf2xjKbg==</Password>
         </AccessData>
         <Properties>
            <Property>
               <Name>maxConnection</Name>
               <Value encrypted="false">20</Value>
            </Property>
            <Property>
               <Name>aquamapsWorldTable</Name>
               <Value encrypted="false">world</Value>
            </Property>
            <Property>
               <Name>aquamapsDataStore</Name>
               <Value encrypted="false">true</Value>
            </Property>
         </Properties>
      </AccessPoint>
   </Profile>


Jackrabbit Repository Runtime Resource

The Jackrabbit Repository Runtime Resource gives information about access to the Jackrabbit repository.

Description

The resource can be registered only at VO level

Fields

In order to be validated by the application, the Runtime Resource must follow these rules :

  • Category = Database
  • Platform/Name = JCR

One Access Points compliant with the following rules is required :

  • Internal logic repository access point :
    • Entry Name
    • user
    • password


Obis plugin Runtime Resource

The Obis plugin Runtime Resource gives information about the Obis database instance: where the database is deployed and what are the credentials to contact it.

Description

There will be one Runtime Resource for database instance.

The resource can be registered;

  • at VO level, if the database instance is shared between VREs.
  • at VRE level, if the database instance is VRE dedicated.

The Obis plugin runtime resource is mandatory if in the VO/VRE is installed the Obis plugin.

Fields

As for all the Species Product Discovery plugins the resource should have the same name of the plugin in this case Obis. Other than required Runtime Resource fields almost one access point is necessary for a Obis plugin Runtime Resource. The access point should have an endpoint with entryname =jdbc with as value a JDBC connection url for the database instance.

Example

    <Profile>
      <Category>BiodiversityRepository</Category>
      <Name>Obis</Name>
      <Description>Obis database coordinates</Description>
      <Platform>
         <Name>Postgresql</Name>
         <Version>8</Version>
         <MinorVersion>4</MinorVersion>
         <RevisionVersion>0</RevisionVersion>
         <BuildVersion>0</BuildVersion>
      </Platform>
      <RunTime>
         <HostedOn>geoserver2.i-marine.research-infrastructures.eu</HostedOn>
         <GHN UniqueID="" />
         <Status>READY</Status>
      </RunTime>
      <AccessPoint>
         <Description>jdbc access point</Description>
         <Interface>
            <Endpoint EntryName="jdbc">jdbc:postgresql://geoserver2.i-marine.research-infrastructures.eu/obis</Endpoint>
         </Interface>
         <AccessData>
            <Username>postgres</Username>
            <Password>***********</Password>
         </AccessData>
      </AccessPoint>
   </Profile>


BrazilianFlora plugin Runtime Resource

The BrazilianFlora plugin Runtime Resource gives the link to FloraBrasil API and the credentials to contact BrazilianFlora database.

Description

Since FloraBrasil API permits to retrieve taxa using just the exact name, specifying its rank, we create a database by Lista de Espécies da Flora do Brasil through FloraBrasil API, which we are using to populate the BrazilianFlora database.

Fields

We have 2 Access Points, with EntryName:

  • "rest": it contains the FloraBrasil API link.
  • "jdbc": it contains the information for JDBC access to the postgres database with Username and Password.

Example

    <Profile>       
      <Category>BiodiversityRepository</Category>     
      <Name>BrazilianFlora</Name>        
      <Description>RuntimeResource for  BrazilianFlora repository</Description>        
      <Platform>            
         <Name>Web Service</Name>            
         <Version>1</Version>            
         <MinorVersion>0</MinorVersion>            
         <RevisionVersion>0</RevisionVersion>            
         <BuildVersion>0</BuildVersion>       
      </Platform>    
      <RunTime>           
         <HostedOn>node24.d.d4science.research-infrastructures.eu</HostedOn>          
         <GHN UniqueID="" />            
         <Status>READY</Status>        
      </RunTime>    
     <AccessPoint>     
         <Description>rest service access point</Description>           
         <Interface>                
            <Endpoint EntryName="rest">http://checklist.florabrasil.net/service/</Endpoint>            
         </Interface>            
         <AccessData>                
            <Username />                
            <Password></Password>            
         </AccessData>        
      </AccessPoint>    
       <AccessPoint>            
         <Description>postgres</Description>            
         <Interface>                
            <Endpoint EntryName="jdbc">jdbc:postgresql://node24.d.d4science.research-infrastructures.eu/brazilianFlora</Endpoint>            
         </Interface>         
         <AccessData>                
            <Username>gcube</Username>              
            <Password>***********</Password>     
         </AccessData>         
         <Properties>         
            <Property>                   
               <Name>hostName</Name>                  
               <Value encrypted="false">node24.d.d4science.research-infrastructures.eu</Value>             
            </Property>          
         </Properties>       
      </AccessPoint>   
   </Profile>

CatalogueOfLife plugin Runtime Resource

The CatalogueOfLife plugin Runtime Resource gives the link to CatalogueOfLife web service which provide programmatic access to the checklist.

Description

For a programmatic access to the CatalogueOfLife Web service we use the Annual Checklist web service available. Using a correctly formatted URL we receive an XML document containing the taxonomic information we require.

Fields

CatalogueOfLife plugin Runtime Resource has a access point and its endpoint has entryname CatalogueOfLife. Its value is a link to CatalogueOfLife web service.


ITIS plugin Runtime Resource

The ITIS plugin Runtime Resource gives the link to ITIS database dump files.

Description

For a programmatic access to ITIS, the Integrated Taxonomic Information System, we download and extract the file on the system we use to load the MySQL database.

Fields

An access point entry, with entry name "jdbc", is required. It contains the information for JDBC access to the database. ITIS plugin Runtime Resource has a access point and its endpoint.

Example

    <Profile>       
      <Category>BiodiversityRepository</Category>     
      <Name>ITIS</Name>       
      <Description>RuntimeResource for ITIS Plugin</Description>  
      <Platform>            
         <Name>MySQL</Name>            
         <Version>5</Version>          
         <MinorVersion>1</MinorVersion>           
         <RevisionVersion>62</RevisionVersion>         
         <BuildVersion>0</BuildVersion>       
      </Platform>     
      <RunTime>           
         <HostedOn>node24.d.d4science.research-infrastructures.eu</HostedOn>          
         <GHN UniqueID="" />            
         <Status>READY</Status>        
      </RunTime>        
       <AccessPoint>            
         <Description>jdbc connection</Description>            
         <Interface>                
            <Endpoint EntryName="jdbc">jdbc:mysql://node24.d.d4science.research-infrastructures.eu/ITIS</Endpoint>            
         </Interface>         
         <AccessData>                
            <Username>itisuser</Username>              
            <Password>***********</Password>     
         </AccessData>         
         <Properties>         
            <Property>                   
               <Name>hostName</Name>                  
               <Value encrypted="false">node24.d.d4science.research-infrastructures.eu</Value>             
            </Property>          
         </Properties>       
      </AccessPoint>   
   </Profile>

SpeciesLink plugin Runtime Resource

The SpeciesLink plugin Runtime Resource gives the link to SpeciesLink web service which provide programmatic access to data.

Description

SpeciesLink plugin data is accessible through programmatic search on a web service interface based on the TAPIR protocol and on the DarwinCore data standard.

Fields

One access point is necessary for a SpeciesLink plugin Runtime Resource.

  • EntryName = tapir
  • Additional Properties:
    • model

The property model contains the output model definition, in this case the DarwinCore data standard.

Example

    <Profile>     
      <Category>BiodiversityRepository</Category>       
      <Name>SpeciesLink</Name>       
      <Description>RuntimeResource for SpeciesLink repository</Description>        
      <Platform>          
         <Name>TapirLink</Name>           
         <Version>0</Version>           
         <MinorVersion>7</MinorVersion>            
         <RevisionVersion>1</RevisionVersion>           
         <BuildVersion>0</BuildVersion>      
      </Platform>       
      <RunTime>            
         <HostedOn>tapir.cria.org.br</HostedOn>            
         <GHN UniqueID="" />            
         <Status>READY</Status>       
      </RunTime>        
      <AccessPoint>           
         <Description>tapir protocol access point</Description>           
         <Interface>                
            <Endpoint EntryName="tapir">http://tapir.cria.org.br/tapirlink/tapir.php/specieslink</Endpoint>            
         </Interface>            
         <AccessData>                
            <Username />               
            <Password>***********</Password>            
         </AccessData>           
         <Properties>              
            <Property>            
               <Name>model</Name>                  
               <Value encrypted="false">http://rs.tdwg.org/tapir/cs/dwc/1.4/model/dw_core_geo_cur.xml</Value>               
            </Property>           
         </Properties>       
      </AccessPoint>   
   </Profile>


Worms plugin Runtime Resource

The WoRMS plugin Runtime Resource gives the link to the WoRMS webservice to feed our application with standard WoRMS taxonomy.

Description

WoRMS webservice currently supports the platform-independent SOAP/WSDL standard. The webservice exposes a standard taxonomy of marine animal species integrated with Global Species Databases (GSD).

Fields

Worms plugin Runtime Resource has an access point and its endpoint has entryname Worms. Its value is a link to Worms web service.


NCBI plugin Runtime Resource

The NCBI plugin Runtime Resource gives the link to NCBI database dump files.

Description

For a programmatic access to NCBI, the National Center for Biotechnology Information, we download and extract the file on the system we use to load the PostgreSQL database.

Fields

NCBI plugin Runtime Resource has 2 Access Points, with EntryName:

  • "ftp": it contains the ftp link to database dump.
  • "jdbc": it contains the information for JDBC access to the postgres database with Username and Password.


IRMNG plugin Runtime Resource

The IRMNG plugin Runtime Resource gives the link to IRMNG database dump files in Darwin Core Archive.

Description

For a programmatic access to IRMNG, the Interim Register of Marine and Nonmarine Genera, we download and extract the file on the system we use to load the PostgreSQL database.

Fields

IRMNG plugin Runtime Resource has 2 Access Points, with EntryName:

  • "dump": it contains the link to database dump.
  • "jdbc": it contains the information for JDBC access to the postgres database with Username and Password.


Storage Manager Runtime Resource

The Storage Manager Runtime Resource gives information about servers backend of storageManager library.

Description

The servers are used to store file by storageManager library. The server descripted can be a only one server or a cluster of server. The runtime resource define the type of the server and the ip address. The resource is registered at VO level

Fields

In order to be validated by the application, the Runtime Resource must follow these rules :

  • Category = DataStorage
  • Name= StorageManager
  • Platform/Name = storage-manager

One Access Points compliant with the following rules is required :

  • Internal logic repository access point :
    • Entry Name: server[i] where i is an integer. This field contains the ip address of the server
    • property host that define the host name of the server
    • property type that define the type of the backend, in this case a MongoDB server

Example

<Resource version="0.4.x">
   <ID>0717b450-a698-11e2-900a-a46c6ff57f05</ID>
   <Type>RuntimeResource</Type>
   <Scopes>
      <Scope>/d4science.research-infrastructures.eu</Scope>
      <Scope>/d4science.research-infrastructures.eu/Ecosystem</Scope>
   </Scopes>
   <Profile>
      <Category>DataStorage</Category>
      <Name>StorageManager</Name>
      <Description>Backend definition  for StorageManager library</Description>
      <Platform>
         <Name>storage-manager</Name>
         <Version>2</Version>
         <MinorVersion>0</MinorVersion>
         <RevisionVersion>0</RevisionVersion>
         <BuildVersion>0</BuildVersion>
      </Platform>
      <RunTime>
         <HostedOn>d4science.org</HostedOn>
         <GHN UniqueID="" />
         <Status>READY</Status>
      </RunTime>
      <AccessPoint>
         <Description>MongoDB server</Description>
         <Interface>
            <Endpoint EntryName="server1">146.48.122.138</Endpoint>
         </Interface>
         <AccessData>
            <Username />
            <Password>6vW1u92cpdgHzYAgIurn9w==</Password>
         </AccessData>
         <Properties>
            <Property>
               <Name>host</Name>
               <Value encrypted="false">node58.p.d4science.research-infrastructures.eu</Value>
            </Property>
            <Property>
               <Name>type</Name>
               <Value encrypted="false">MongoDB</Value>
            </Property>
         </Properties>
      </AccessPoint>
      <AccessPoint>
         <Description>MongoDB server</Description>
         <Interface>
            <Endpoint EntryName="server2">146.48.122.153</Endpoint>
         </Interface>
         <AccessData>
            <Username />
            <Password>6vW1u92cpdgHzYAgIurn9w==</Password>
         </AccessData>
         <Properties>
            <Property>
               <Name>host</Name>
               <Value encrypted="false">node67.p.d4science.research-infrastructures.eu</Value>
            </Property>
            <Property>
               <Name>type</Name>
               <Value encrypted="false">MongoDB</Value>
            </Property>
         </Properties>
      </AccessPoint>
      <AccessPoint>
         <Description>MongoDB server</Description>
         <Interface>
            <Endpoint EntryName="server3">146.48.122.102</Endpoint>
         </Interface>
         <AccessData>
            <Username />
            <Password>6vW1u92cpdgHzYAgIurn9w==</Password>
         </AccessData>
         <Properties>
            <Property>
               <Name>host</Name>
               <Value encrypted="false">node80.p.d4science.research-infrastructures.eu</Value>
            </Property>
            <Property>
               <Name>type</Name>
               <Value encrypted="false">MongoDB</Value>
            </Property>
         </Properties>
      </AccessPoint>
   </Profile>
</Resource>

Maven Repository Runtime Resource

The Maven Repository Runtime Resource gives information about a Maven Repository instance providing this info:

  • Host where the repository is deployed (mandatory)
  • Endpoints
    • Maven repo endpoint (mandatory)
    • Other endpoints (like the nexus browser url)

Description

There will be one Runtime Resource for each repository instance.

The resource can be registered;

  • at ROOT level, if the repository instance is shared for the entire infrastructure.
  • at VO level, if the repository instance is shared between VREs.
  • at VRE level, if the repository instance is VRE dedicated.

The Maven Repository runtime resource is mandatory if in the Infrastructure/VO/VRE is installed:

  • War Management Portlet
  • Software Upload Wizard Portlet

Fields

The Runtime Resource must have:

  • Category: Maven
  • Name: MavenRepository
  • Runtime tag filled with data regarding the host where the repository is hosted.
  • An access point pointing to the root repository URL with these characteristics:

Example

   <Profile>
      <Category>Maven</Category>
      <Name>MavenRepository</Name>
      <Description>Maven Repository information</Description>
      <Platform>
         <Name>Nexus</Name>
         <Version>1</Version>
         <MinorVersion>0</MinorVersion>
         <RevisionVersion>0</RevisionVersion>
         <BuildVersion>0</BuildVersion>
      </Platform>
      <RunTime>
         <HostedOn>maven.research-infrastructures.eu</HostedOn>
         <GHN UniqueID="" />
         <Status>READY</Status>
      </RunTime>
      <AccessPoint>
         <Description>RepositoryUrl</Description>
         <Interface>
            <Endpoint EntryName="RepositoryUrl">http://maven.research-infrastructures.eu:8081/nexus/content/repositories/gcube-snapshots/</Endpoint>
         </Interface>
         <AccessData>
            <Username />
            <Password>*************</Password>
         </AccessData>
         <Properties>
            <Property>
               <Name>repositoryId</Name>
               <Value encrypted="false">gcube-snapshots</Value>
            </Property>
         </Properties>
      </AccessPoint>
      <AccessPoint>
         <Description>Nexus Browser Url</Description>
         <Interface>
            <Endpoint EntryName="NexusUrl">http://maven.research-infrastructures.eu/nexus/index.html#view-repositories;gcube-snapshots~browsestorage</Endpoint>
         </Interface>
         <AccessData>
            <Username />
            <Password>**************</Password>
         </AccessData>
      </AccessPoint>
   </Profile>
Retrieved from "https://gcube.wiki.gcube-system.org/index.php?title=RuntimeResourceClassification&oldid=24782"