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ecological-engine-wps-extension
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git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineWPSExtension@91647 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Gianpaolo Coro 2014-02-14 15:51:06 +00:00
parent 6e7147c050
commit 703e0e96d6
20 changed files with 3968 additions and 0 deletions
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8
.classpath Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" output="target/classes" path="src/main/java"/>
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"/>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
<classpathentry kind="output" path="target/classes"/>
</classpath>

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.project Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>EcologicalEngineWPSExtension</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.m2e.core.maven2Builder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
</projectDescription>

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.settings/org.eclipse.jdt.core.prefs Normal file
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#Mon Feb 10 17:08:17 CET 2014
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=1.5
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.source=1.5

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.settings/org.eclipse.m2e.core.prefs Normal file
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#Mon Feb 10 17:08:16 CET 2014
activeProfiles=
eclipse.preferences.version=1
resolveWorkspaceProjects=true
version=1

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cfg/ALog.properties Normal file
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#### Use two appenders, one to log to console, another to log to a file
log4j.rootCategory= R
#### First appender writes to console
log4j.appender.stdout=org.apache.log4j.ConsoleAppender
log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
log4j.appender.stdout.layout.ConversionPattern=%d{dd/MM/yyyy HH:mm:ss} %p %t %c - %m%n
#log4j.appender.stdout.layout.ConversionPattern=%m%n
#log4j.appender.stdout.File=Analysis.log
#### Second appender writes to a file
log4j.logger.AnalysisLogger=trace, stdout,R
log4j.appender.R=org.apache.log4j.RollingFileAppender
log4j.appender.R.File=Analysis.log
log4j.appender.R.MaxFileSize=50000KB
log4j.appender.R.MaxBackupIndex=2
log4j.appender.R.layout=org.apache.log4j.PatternLayout
log4j.appender.R.layout.ConversionPattern=%d{dd/MM/yyyy HH:mm:ss} %p %t %c - %m%n
#log4j.appender.R.layout.ConversionPattern=%m%n
#### Third appender writes to a file
log4j.logger.org.hibernate=H
#log4j.appender.H=org.apache.log4j.RollingFileAppender
log4j.appender.H=org.apache.log4j.AsyncAppender
#log4j.appender.H.File=HibernateLog.log
#log4j.appender.H.MaxFileSize=1024KB
#log4j.appender.H.MaxBackupIndex=2
log4j.appender.H.layout=org.apache.log4j.PatternLayout
log4j.appender.H.layout.ConversionPattern=%d{dd/MM/yyyy HH:mm:ss} %p %t %c - %m%n

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cfg/DestinationDBHibernate.cfg.xml Normal file
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<?xml version='1.0' encoding='UTF-8'?>
<hibernate-configuration>
<session-factory>
<property name="connection.driver_class">org.postgresql.Driver</property>
<property name="connection.provider_class">org.hibernate.connection.C3P0ConnectionProvider</property>
<property name="connection.url">jdbc:postgresql://localhost/testdb</property>
<property name="connection.username">gcube</property>
<property name="connection.password">d4science2</property>
<!-- <property name="dialect">org.hibernatespatial.postgis.PostgisDialect</property>-->
<property name="dialect">org.hibernate.dialect.PostgreSQLDialect</property>
<property name="transaction.factory_class">org.hibernate.transaction.JDBCTransactionFactory</property>
<property name="c3p0.timeout">0</property>
<property name="c3p0.max_size">1</property>
<property name="c3p0.max_statements">0</property>
<property name="c3p0.min_size">1</property>
<property name="current_session_context_class">thread</property>
</session-factory>
</hibernate-configuration>

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cfg/algorithms.properties Normal file
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AQUAMAPS_SUITABLE=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsSuitable
AQUAMAPS_NATIVE=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNative
AQUAMAPS_NATIVE_2050=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNative2050
AQUAMAPS_SUITABLE_2050=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsSuitable2050
AQUAMAPS_NATIVE_NEURALNETWORK=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNN
AQUAMAPS_SUITABLE_NEURALNETWORK=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNNSuitable
FEED_FORWARD_A_N_N_DISTRIBUTION=org.gcube.dataanalysis.ecoengine.spatialdistributions.FeedForwardNeuralNetworkDistribution

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cfg/clusterers.properties Normal file
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DBSCAN=org.gcube.dataanalysis.ecoengine.clustering.DBScan
LOF=org.gcube.dataanalysis.ecoengine.clustering.LOF
KMEANS=org.gcube.dataanalysis.ecoengine.clustering.KMeans
XMEANS=org.gcube.dataanalysis.ecoengine.clustering.XMeansWrapper

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cfg/dynamictransducerers.properties Normal file
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org.gcube.dataanalysis.geo.wps.factory.DynamicWPSTransducerer

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cfg/evaluators.properties Normal file
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DISCREPANCY_ANALYSIS=org.gcube.dataanalysis.ecoengine.evaluation.DiscrepancyAnalysis
QUALITY_ANALYSIS=org.gcube.dataanalysis.ecoengine.evaluation.DistributionQualityAnalysis
HRS=org.gcube.dataanalysis.ecoengine.evaluation.HabitatRepresentativeness

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cfg/generators.properties Normal file
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LOCAL_WITH_DATABASE=org.gcube.dataanalysis.ecoengine.processing.LocalSplitGenerator
SIMPLE_LOCAL=org.gcube.dataanalysis.ecoengine.processing.LocalSimpleSplitGenerator

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cfg/modelers.properties Normal file
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HSPEN_MODELER=org.gcube.dataanalysis.ecoengine.modeling.SimpleModeler

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cfg/models.properties Normal file
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HSPEN=org.gcube.dataanalysis.ecoengine.models.ModelHSPEN
AQUAMAPSNN=org.gcube.dataanalysis.ecoengine.models.ModelAquamapsNN
FEED_FORWARD_ANN=org.gcube.dataanalysis.ecoengine.models.FeedForwardNN
FEED_FORWARD_ANN_FILE=org.gcube.dataanalysis.ecoengine.models.testing.FeedForwardNNFile

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cfg/nodealgorithms.properties Normal file
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AQUAMAPS_SUITABLE=org.gcube.dataanalysis.peeng.models.AquamapsSuitableNode

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cfg/operators.xml Normal file
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cfg/test.xml Normal file
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<xml-fragment statusSupported="false" storeSupported="true" wps:processVersion="1.0.0" xmlns:ows="http://www.opengis.net/ows/1.1" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:wps="http://www.opengis.net/wps/1.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<ows:Identifier>Buffer</ows:Identifier>
<ows:Title>Create a buffer around a polygon.</ows:Title>
<ows:Abstract>Create a buffer around a single polygon. Accepts the polygon as GML and provides GML output for the buffered feature.</ows:Abstract>
<ows:Metadata xlink:title="spatial"/>
<ows:Metadata xlink:title="geometry"/>
<ows:Metadata xlink:title="buffer"/>
<ows:Metadata xlink:title="GML"/>
<wps:Profile>urn:ogc:wps:1.0.0:buffer</wps:Profile>
<wps:WSDL xlink:href="http://foo.bar/foo"/>
<DataInputs>
<Input minOccurs="1" maxOccurs="1">
<ows:Identifier>InputPolygon</ows:Identifier>
<ows:Title>Polygon to be buffered</ows:Title>
<ows:Abstract>URI to a set of GML that describes the polygon.</ows:Abstract>
<ComplexData maximumMegabytes="5">
<Default>
<Format>
<MimeType>text/xml</MimeType>
<Encoding>base64</Encoding>
<Schema>http://foo.bar/gml/3.1.0/polygon.xsd</Schema>
</Format>
</Default>
<Supported>
<Format>
<MimeType>text/xml</MimeType>
<Encoding>UTF-8</Encoding>
<Schema>http://foo.bar/gml/3.1.0/polygon.xsd</Schema>
</Format>
</Supported>
</ComplexData>
</Input>
<Input minOccurs="0" maxOccurs="1">
<ows:Identifier>BufferDistance</ows:Identifier>
<ows:Title>Buffer Distance</ows:Title>
<ows:Abstract>Distance to be used to calculate buffer.</ows:Abstract>
<LiteralData>
<ows:DataType ows:reference="http://www.w3.org/TR/xmlschema-2/#float">float</ows:DataType>
<UOMs>
<Default>
<ows:UOM>meters</ows:UOM>
</Default>
<Supported>
<ows:UOM>meters</ows:UOM>
<ows:UOM>feet</ows:UOM>
</Supported>
</UOMs>
<ows:AnyValue/>
<DefaultValue>100</DefaultValue>
</LiteralData>
</Input>
</DataInputs>
<ProcessOutputs>
<Output>
<ows:Identifier>BufferedPolygon</ows:Identifier>
<ows:Title>Buffered Polygon</ows:Title>
<ows:Abstract>GML stream describing the buffered polygon feature.</ows:Abstract>
<ComplexOutput>
<Default>
<Format>
<MimeType>text/xml</MimeType>
<Encoding>base64</Encoding>
<Schema>http://foo.bar/gml/3.1.0/polygon.xsd</Schema>
</Format>
</Default>
<Supported>
<Format>
<MimeType>text/xml</MimeType>
<Encoding>UTF-8</Encoding>
<Schema>http://foo.bar/gml/3.1.0/polygon.xsd</Schema>
</Format>
</Supported>
</ComplexOutput>
</Output>
</ProcessOutputs>
</xml-fragment>

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cfg/transducerers.properties Normal file
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ABSENCE_CELLS_FROM_AQUAMAPS=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.MarineAbsencePointsFromAquamapsDistribution
BIOCLIMATE_HSPEC=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHSPECTransducer
BIOCLIMATE_HCAF=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHCAFTransducer
BIOCLIMATE_HSPEN=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHSPENTransducer
HCAF_INTERPOLATION=org.gcube.dataanalysis.ecoengine.transducers.InterpolationTransducer
HCAF_FILTER=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.HcafFilter
HSPEN_FILTER=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.HspenFilter
OCCURRENCES_MERGER=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsMerger
OCCURRENCES_INTERSECTOR=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsIntersector
OCCURRENCES_MARINE_TERRESTRIAL=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsInSeaOnEarth
OCCURRENCES_DUPLICATES_DELETER=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsDuplicatesDeleter
OCCURRENCES_SUBTRACTION=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsSubtraction
PRESENCE_CELLS_GENERATION=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.MarinePresencePoints
FIN_TAXA_MATCH=org.gcube.dataanalysis.fin.taxamatch.TaxaMatchTransducer

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cfg/userperspective.properties Normal file
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ANOMALIES_DETECTION=DBSCAN,LOF,KMEANS,XMEANS
CLASSIFICATION=FEED_FORWARD_A_N_N_DISTRIBUTION
CLIMATE=BIOCLIMATE_HSPEC,BIOCLIMATE_HCAF,BIOCLIMATE_HSPEN,HCAF_INTERPOLATION
CORRELATION_ANALYSIS=HRS
DATA_CLUSTERING=DBSCAN,KMEANS,XMEANS
FILTERING=HCAF_FILTER,HSPEN_FILTER
FUNCTION_SIMULATION=FEED_FORWARD_A_N_N_DISTRIBUTION
OCCURRENCES=ABSENCE_CELLS_FROM_AQUAMAPS,PRESENCE_CELLS_GENERATION,OCCURRENCES_MERGER,OCCURRENCES_INTERSECTOR,OCCURRENCES_MARINE_TERRESTRIAL,OCCURRENCES_DUPLICATES_DELETER,OCCURRENCES_SUBTRACTION
PERFORMANCES_EVALUATION=QUALITY_ANALYSIS,DISCREPANCY_ANALYSIS
SPECIES_SIMULATION=AQUAMAPS_SUITABLE,AQUAMAPS_NATIVE,AQUAMAPS_NATIVE_2050,AQUAMAPS_SUITABLE_2050,AQUAMAPS_NATIVE_NEURALNETWORK,AQUAMAPS_SUITABLE_NEURALNETWORK
TRAINING=HSPEN,AQUAMAPSNN,FEED_FORWARD_ANN
TIME_SERIES=HCAF_INTERPOLATION
TAXA=FIN_TAXA_MATCH

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pom.xml Normal file
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-wps-extension</artifactId>
<version>1.0.0-SNAPSHOT</version>
<name>ecological-engine-wps-extension</name>
<description>ecological-engine-wps-extension</description>
<properties>
<distroDirectory>${project.basedir}/distro</distroDirectory>
</properties>
<dependencies>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>EcologicalEngineExecutor</artifactId>
<version>[1.6.0-SNAPSHOT,2.0.0)</version>
</dependency>
<!-- <dependency> <groupId>org.n52.wps</groupId> <artifactId>52n-wps-client-lib</artifactId>
<version>3.0</version> </dependency> -->
<dependency>
<groupId>org.n52.wps</groupId>
<artifactId>52n-wps-client-lib</artifactId>
<version>3.2.0</version>
</dependency>
</dependencies>
<repositories>
<repository>
<id>52north-releases</id>
<name>52north-releases</name>
<url>http://maven.research-infrastructures.eu/nexus/content/repositories/52north-releases/</url>
</repository>
<repository>
<id>n52-snapshots</id>
<name>n52-snapshots</name>
<url>http://52north.org/maven/repo/snapshots/</url>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
</repositories>
</project>

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src/main/resources/wps_config.xml Normal file
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