Add TrendyLyzer and species/taxa algorithms; change version 1.0.0-> 1.1.0
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineExternalAlgorithms@79495 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Angela Italiano
parent
91a15af3f8
commit
14e04746c9
25
.classpath
25
.classpath
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@ -1,7 +1,26 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<classpath>
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<classpathentry kind="src" output="target/classes" path="src/main/java"/>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
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<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
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<classpathentry kind="src" output="target/classes" path="src/main/java">
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<attributes>
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<attribute name="optional" value="true"/>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
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<attributes>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
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<attributes>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="src" output="target/test-classes" path="src/test/java">
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<attributes>
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<attribute name="optional" value="true"/>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="output" path="target/classes"/>
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</classpath>
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@ -4,4 +4,7 @@
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date="2013-03-19">
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<Change>First Release</Change>
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</Changeset>
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<Changeset component="${build.finalName}" date="2013-07-22">
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<Change>Add TrendyLyzer algorithms and species/taxa procedures </Change>
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</Changeset>
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</ReleaseNotes>
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@ -6,7 +6,7 @@
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<Description>Ecological Engine Library</Description>
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<Class>EcologicalEngineExternalAlgorithms</Class>
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<Name>${artifactId}</Name>
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<Version>1.0.0</Version>
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<Version>1.1.0</Version>
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<Packages>
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<Software>
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<Name>${artifactId}</Name>
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102
pom.xml
102
pom.xml
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@ -9,7 +9,7 @@
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</parent>
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<groupId>org.gcube.dataanalysis</groupId>
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<artifactId>ecological-engine-external-algorithms</artifactId>
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<version>1.0.0-SNAPSHOT</version>
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<version>1.1.0</version>
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<name>ecological-engine-external-algorithms</name>
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<description>ecological-engine-external-algorithms library</description>
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<properties>
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@ -20,12 +20,6 @@
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<groupId>org.gcube.dataanalysis</groupId>
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<artifactId>ecological-engine</artifactId>
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<version>1.7.0-SNAPSHOT</version>
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<exclusions>
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<exclusion>
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<artifactId>slf4j-log4j12</artifactId>
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<groupId>org.slf4j</groupId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>postgresql</groupId>
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@ -33,10 +27,98 @@
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<version>8.4-702.jdbc4</version>
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</dependency>
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<dependency>
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<groupId>ch.qos.logback</groupId>
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<artifactId>logback-classic</artifactId>
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<version>1.0.9</version>
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<groupId>org.gcube.common</groupId>
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<artifactId>rapidminer-custom</artifactId>
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<version>1.2.0-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.gcube.core</groupId>
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<artifactId>common-gcore-stubs</artifactId>
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<version>[1.0.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
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</dependency>
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<dependency>
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<groupId>org.gcube.core</groupId>
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<artifactId>common-encryption</artifactId>
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<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
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</dependency>
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<dependency>
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<groupId>org.gcube.core</groupId>
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<artifactId>common-scope-maps</artifactId>
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<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
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</dependency>
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<dependency>
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<groupId>org.gcube.data.spd</groupId>
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<artifactId>spd-client-library</artifactId>
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<version>[3.0.0-SNAPSHOT, 4.0.0-SNAPSHOT)</version>
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<scope>provided</scope>
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</dependency>
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<!-- This dependency is needed and is need on TOP to use GWT UI BInder
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without old Xerces version of gCore complaining -->
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<dependency>
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<groupId>xerces</groupId>
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<artifactId>xercesImpl</artifactId>
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<version>2.9.1</version>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>org.gcube.data.spd</groupId>
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<artifactId>spql-parser</artifactId>
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<version>[2.0.0-SNAPSHOT, 3.0.0-SNAPSHOT)</version>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>org.gcube.common</groupId>
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<artifactId>csv4j</artifactId>
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<version>[1.1.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>org.gcube.data.spd</groupId>
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<artifactId>spd-model</artifactId>
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<version>[1.0.0-SNAPSHOT, 3.0.0-SNAPSHOT)</version>
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<!-- <version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version> -->
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<!-- UNCOMMENT THIS FOR RELEASE -->
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>org.gcube.resources.discovery</groupId>
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<artifactId>discovery-client</artifactId>
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<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>org.gcube.core</groupId>
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<artifactId>common-clients</artifactId>
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<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
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</dependency>
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<dependency>
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<groupId>org.gcube.core</groupId>
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<artifactId>common-fw-clients</artifactId>
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<version>1.0.0-SNAPSHOT</version>
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<scope>runtime</scope>
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</dependency>
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<dependency>
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<groupId>org.gcube.resources.discovery</groupId>
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<artifactId>ic-client</artifactId>
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<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
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</dependency>
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<dependency>
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<groupId>org.gcube.core</groupId>
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<artifactId>common-scope-maps</artifactId>
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<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
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</dependency>
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</dependencies>
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<repositories>
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<repository>
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@ -0,0 +1,13 @@
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package org.gcube.dataanalysis.JobSMspd;
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/**
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* Hello world!
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*
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*/
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public class App
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{
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public static void main( String[] args )
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{
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System.out.println( "Hello World!" );
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}
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}
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@ -0,0 +1,7 @@
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package org.gcube.dataanalysis.JobSMspd;
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public enum ExpandOption {
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EXPAND,
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NOT_EXPAND
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}
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@ -0,0 +1,485 @@
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package org.gcube.dataanalysis.JobSMspd;
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import static org.gcube.data.spd.client.plugins.AbstractPlugin.manager;
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import java.io.BufferedWriter;
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import java.io.File;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.lang.reflect.Field;
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import java.sql.Connection;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.sql.Statement;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.LinkedHashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import org.gcube.common.scope.api.ScopeProvider;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.data.spd.client.proxies.Manager;
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import org.gcube.data.spd.model.Conditions;
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import org.gcube.data.spd.model.PluginDescription;
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import org.gcube.data.spd.model.util.Capabilities;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.ColumnTypesList;
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import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
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import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
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import org.gcube.dataanalysis.ecoengine.datatypes.OutputTable;
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import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
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import org.gcube.dataanalysis.ecoengine.datatypes.ServiceType;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.ServiceParameters;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
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import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
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import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory;
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import org.gcube.dataanalysis.ecoengine.utils.DatabaseUtils;
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import org.gcube.dataanalysis.ecoengine.utils.DynamicEnum;
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import org.hibernate.SessionFactory;
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public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
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LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
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static String databaseParameterName = "FishBase";
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static String userParameterName = "user";
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static String passwordParameterName = "password";
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static String urlParameterName = "FishBase";
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SessionFactory dbconnection = null;
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public static boolean call=false;
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String tablename;
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String columnnames;
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List<Object> speciesList;
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protected String fileName;
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BufferedWriter out;
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String outputtablename;
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String outputErrortablename;
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String outputtable;
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HashMap<String, String>dpHash= new HashMap<String, String>();
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HashMap<String, String>dpUHash= new HashMap<String, String>();
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HashMap<String, String>dpEHash= new HashMap<String, String>();
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String tableError;
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private DataPenum dp = new DataPenum();
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private ExtentionDPEnum dpE = new ExtentionDPEnum();
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private UnfoldDPEnum dpU = new UnfoldDPEnum();
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private String dataProvider = "Data Provider :";
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private String chosendataProvider = new String();
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private String dataProviderExtention = "Data Provider (Expand Option):";
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private String chosendataProviderExtention=new String();
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//private String chosendataProviderUnfold="Data Provider Unfold:";
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private String dataProviderUnfold = "Data Provider (Unfold Option):";
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private String chosendataProviderUnfold=new String();
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@Override
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public String getDescription() {
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return "An algorithm that once data provider and search options are selecteced, it has to return the occurrences";
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}
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@Override
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public void init() throws Exception {
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AnalysisLogger.getLogger().debug("SMFaoAlg");
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}
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public void fulfilParameters() throws IOException {
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config.setParam("DatabaseDriver", "org.postgresql.Driver");
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dbconnection = DatabaseUtils.initDBSession(config);
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tablename = getInputParameter("SpeciesTable");
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columnnames = getInputParameter("SpeciesColumns");
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outputtablename = getInputParameter("OutputTableName");
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outputtable = getInputParameter("OutputTable");
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tableError = getInputParameter("ErrorTable");
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chosendataProviderUnfold = getInputParameter(dataProviderUnfold);
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chosendataProviderExtention = getInputParameter(dataProviderExtention);
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chosendataProvider = getInputParameter(dataProvider);
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outputErrortablename = getInputParameter("ErrorTableName");
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String[] columnlist = columnnames.split(AlgorithmConfiguration
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.getListSeparator());
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speciesList = DatabaseFactory.executeSQLQuery("select " + columnlist[0]
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+ " from " + tablename, dbconnection);
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fileName = super.config.getPersistencePath() + "results.csv";
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out = new BufferedWriter(new FileWriter(fileName));
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}
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@Override
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protected void process() throws Exception {
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try {
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fulfilParameters();
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createTables();
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int lenght = (int) (speciesList.size() / 3);
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ArrayList<String> chunk1 = new ArrayList<String>();
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ArrayList<String> chunk2 = new ArrayList<String>();
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ArrayList<String> chunk3 = new ArrayList<String>();
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for (int i = 0; i < speciesList.size(); i++) {
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if (i < lenght)
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chunk1.add((String) speciesList.get(i));
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if (i >= lenght && i <= 2 * lenght)
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chunk2.add((String) speciesList.get(i));
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if (i > 2 * lenght)
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chunk3.add((String) speciesList.get(i));
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}
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ThreadExtractionOccFromSPD t1 = new ThreadExtractionOccFromSPD(
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chunk1, chosendataProvider,chosendataProviderExtention,chosendataProviderUnfold);
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ThreadExtractionOccFromSPD t2 = new ThreadExtractionOccFromSPD(
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chunk2, chosendataProvider,chosendataProviderExtention,chosendataProviderUnfold);
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ThreadExtractionOccFromSPD t3 = new ThreadExtractionOccFromSPD(
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chunk3, chosendataProvider,chosendataProviderExtention,chosendataProviderUnfold);
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Thread th1 = new Thread(t1);
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th1.start();
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Thread th2 = new Thread(t2);
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th2.start();
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Thread th3 = new Thread(t3);
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th3.start();
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th1.join();
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th2.join();
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th3.join();
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write("scientific_name; author; catalogue_number; citation; collection_gode; cordinate_uncertaninty_in_meters; country;"
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+ "credits; family; id; institution_code; kingdom; locality; providere; latitude; longitude; max_depth; min_depth");
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||||
out.newLine();
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insertInTheTable(t1.getInfo());
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insertInTheTable(t2.getInfo());
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insertInTheTable(t3.getInfo());
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|
||||
insertInTheTableErrors(t1.getErrors());
|
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insertInTheTableErrors(t2.getErrors());
|
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insertInTheTableErrors(t3.getErrors());
|
||||
|
||||
} catch (Exception e) {
|
||||
e.printStackTrace();
|
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throw e;
|
||||
} finally {
|
||||
DatabaseUtils.closeDBConnection(dbconnection);
|
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out.close();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private void createTables() throws Exception {
|
||||
// String s =
|
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// " (scientific_name character varying, author character varying,catalogue_number character varying, citation character varying,"
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// +
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||||
// "collection_gode character varying,cordinate_uncertaninty_in_meters character varying,country character varying,credits character varying ,family character varying, id character varying, institution_code character varying,kingdom character varying,"
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// +
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// "locality character varying,providere character varying ,latitude character varying, longitude character varying ,max_depth character varying ,min_depth character varying)";
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||||
//
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||||
// DatabaseFactory.executeSQLUpdate("create table " + outputtable + s,
|
||||
// dbconnection);
|
||||
|
||||
DatabaseFactory.executeSQLUpdate("create table " + tableError
|
||||
+ " (error character varying)", dbconnection);
|
||||
}
|
||||
|
||||
private void insertInTheTable(ArrayList<ArrayList<String>> arrays)
|
||||
throws Exception {
|
||||
// AnalysisLogger.getLogger().debug("inside insertInTheTable ");
|
||||
// String st =
|
||||
// " (scientific_name, author,catalogue_number, citation,collection_gode,cordinate_uncertaninty_in_meters,country,"
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||||
// + "credits,family,id,"
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||||
// +
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||||
// " institution_code,kingdom,locality,providere,latitude, longitude,max_depth,min_depth)";
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||||
|
||||
for (ArrayList<String> array : arrays) {
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||||
// String query = "insert into " + outputtable + st + " values (";
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||||
String writeString = new String();
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||||
int i = 0;
|
||||
|
||||
for (String s : array) {
|
||||
if (i != 0) {
|
||||
writeString = writeString + "; ";
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||||
}
|
||||
// query = query + ", ";}
|
||||
writeString = writeString + " '";
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||||
// query = query + " '";
|
||||
if (s != null)
|
||||
s = s.replace("'", "");
|
||||
writeString = writeString + s;
|
||||
// query = query + s;
|
||||
// query = query + "'";
|
||||
writeString = writeString + "'";
|
||||
i++;
|
||||
|
||||
}
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||||
write(writeString);
|
||||
out.newLine();
|
||||
// query = query + ")";
|
||||
// /* DatabaseFactory.executeSQLUpdate(query, dbconnection);*/
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private void insertInTheTableErrors(ArrayList<String> arrays)
|
||||
throws Exception {
|
||||
if (arrays != null) {
|
||||
String st = " (error)";
|
||||
for (String er : arrays) {
|
||||
String query = "insert into " + tableError + st + " values ('"
|
||||
+ er + "')";
|
||||
AnalysisLogger.getLogger().debug("query error : " + query);
|
||||
DatabaseFactory.executeSQLUpdate(query, dbconnection);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public void print(ArrayList<ArrayList<String>> arrays) {
|
||||
for (ArrayList<String> array : arrays) {
|
||||
|
||||
for (String s : array) {
|
||||
AnalysisLogger.getLogger().debug(s);
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
|
||||
}
|
||||
public void setDynamicParameter() {
|
||||
AnalysisLogger.getLogger().debug("Inside setDynamicParameter");
|
||||
ScopeProvider.instance.set("/gcube/devsec");
|
||||
Manager manager = null;
|
||||
|
||||
manager = manager().build();
|
||||
AnalysisLogger.getLogger().debug("costruito manager");
|
||||
AnalysisLogger.getLogger().debug("prima dei plugin");
|
||||
List<PluginDescription> plugin = manager.getPluginsDescription();
|
||||
AnalysisLogger.getLogger().debug("preso i plugin");
|
||||
// if(!dpHash.containsKey("ALL"))
|
||||
// {
|
||||
// dpHash.put("ALL", "ALL");
|
||||
// dp.addEnum(DataProvidersType.class, "ALL");
|
||||
// }
|
||||
// if(!dpUHash.containsKey("ALL"))
|
||||
// {
|
||||
// dpUHash.put("ALL", "ALL");
|
||||
// dpU.addEnum(UnfoldDPEnumType.class, "ALL");
|
||||
// }
|
||||
// if(!dpEHash.containsKey("ALL"))
|
||||
// {
|
||||
// dpEHash.put("ALL", "ALL");
|
||||
// dpE.addEnum(ExtentionDPType.class, "ALL");
|
||||
// }
|
||||
|
||||
dp.addEnum(DataProvidersType.class, "ALL");
|
||||
//dpU.addEnum(UnfoldDPEnumType.class, "ALL");
|
||||
dpE.addEnum(ExtentionDPType.class, "ALL");
|
||||
dpU.addEnum(UnfoldDPEnumType.class, "NO OPTION");
|
||||
dpE.addEnum(ExtentionDPType.class, "NO OPTION");
|
||||
|
||||
|
||||
if (plugin != null) {
|
||||
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"*****PluginDescription is NOT null - length: "
|
||||
+ plugin.size());
|
||||
|
||||
for (int i = 0; i < plugin.size(); i++) {
|
||||
|
||||
PluginDescription pluginDescription = plugin.get(i);
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"For plugin ***"+pluginDescription.getName() );
|
||||
Map<Capabilities, List<Conditions>> pluginCapabilities = pluginDescription
|
||||
.getSupportedCapabilities();
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"created maps");
|
||||
AnalysisLogger.getLogger().debug(
|
||||
" map size"+pluginCapabilities.size());
|
||||
|
||||
for (Entry<Capabilities, List<Conditions>> pluginCapability : pluginCapabilities
|
||||
.entrySet()) {
|
||||
|
||||
Capabilities capability = pluginCapability.getKey();
|
||||
AnalysisLogger.getLogger().debug(
|
||||
capability.name().toString());
|
||||
if(capability.name().toString().equals("Unfold"))
|
||||
{
|
||||
// if(!dpUHash.containsKey(pluginDescription.getName()))
|
||||
// {
|
||||
// AnalysisLogger.getLogger().debug("insert "+
|
||||
// pluginDescription.getName().toString() + "fopr upfold");
|
||||
// dpUHash.put(pluginDescription.getName(), pluginDescription.getName());
|
||||
// dpU.addEnum(UnfoldDPEnumType.class,pluginDescription.getName().toString() );
|
||||
// }
|
||||
dpU.addEnum(UnfoldDPEnumType.class,pluginDescription.getName().toString() );
|
||||
}
|
||||
|
||||
if(capability.name().toString().equals("Expansion"))
|
||||
{
|
||||
// if(!dpEHash.containsKey(pluginDescription.getName()))
|
||||
// {
|
||||
// AnalysisLogger.getLogger().debug("insert "+
|
||||
// pluginDescription.getName().toString() + "fopr Expansion");
|
||||
// dpEHash.put(pluginDescription.getName(), pluginDescription.getName());
|
||||
// dpE.addEnum(ExtentionDPType.class,pluginDescription.getName().toString() );
|
||||
// }
|
||||
dpE.addEnum(ExtentionDPType.class,pluginDescription.getName().toString() );
|
||||
|
||||
}
|
||||
if(capability.name().toString().equals("Occurrence"))
|
||||
{
|
||||
// if(!dpHash.containsKey(pluginDescription.getName()))
|
||||
// {
|
||||
// AnalysisLogger.getLogger().debug("insert "+
|
||||
// pluginDescription.getName().toString() + "fopr Occurrence");
|
||||
// dpHash.put(pluginDescription.getName() , pluginDescription.getName() );
|
||||
// dp.addEnum(DataProvidersType.class,pluginDescription.getName().toString());
|
||||
// }
|
||||
dp.addEnum(DataProvidersType.class,pluginDescription.getName().toString());
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
} else
|
||||
AnalysisLogger.getLogger().debug("*****PluginDescription is null");
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
try{
|
||||
AnalysisLogger.getLogger().debug("inside setInputParameters ");
|
||||
|
||||
addRemoteDatabaseInput(databaseParameterName, urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
List<TableTemplates> templates = new ArrayList<TableTemplates>();
|
||||
templates.add(TableTemplates.GENERIC);
|
||||
InputTable tinput = new InputTable(templates, "SpeciesTable",
|
||||
"The table containing the species information");
|
||||
ColumnTypesList columns = new ColumnTypesList("SpeciesTable",
|
||||
"SpeciesColumns", "Select the columns for species name", false);
|
||||
addStringInput("OutputTableName", "The name of the output table",
|
||||
"occ_");
|
||||
addStringInput("ErrorTableName", "The name of the output table", "err_");
|
||||
ServiceType randomstring = new ServiceType(
|
||||
ServiceParameters.RANDOMSTRING, "OutputTable", "", "occ");
|
||||
ServiceType randomstringErr = new ServiceType(
|
||||
ServiceParameters.RANDOMSTRING, "ErrorTable", "", "err");
|
||||
|
||||
|
||||
AnalysisLogger.getLogger().debug("before setDynamicParameter() ");
|
||||
if(!call)
|
||||
setDynamicParameter();
|
||||
|
||||
// try {
|
||||
//// if (justcall == 0) {
|
||||
//// justcall = 1;
|
||||
//
|
||||
//// }
|
||||
// } catch (Throwable e) {
|
||||
// e.printStackTrace();
|
||||
// AnalysisLogger.getLogger().debug(e.toString());
|
||||
// }
|
||||
|
||||
addEnumerateInput(DataProvidersType.values(), dataProvider,
|
||||
"Choose Data Providere", "ALL");
|
||||
AnalysisLogger.getLogger().debug("Dopo DataProvidersType");
|
||||
addEnumerateInput(ExtentionDPType.values(),dataProviderExtention ,
|
||||
"Choose Expand Option Data Providere","ALL");
|
||||
AnalysisLogger.getLogger().debug("Dopo ExtentionDPType");
|
||||
addEnumerateInput(UnfoldDPEnumType.values(), dataProviderUnfold,
|
||||
"Choose UnfoldRR Option Data Providere","ALL");
|
||||
AnalysisLogger.getLogger().debug("Dopo UnfoldDPEnumType");
|
||||
|
||||
|
||||
inputs.add(tinput);
|
||||
inputs.add(columns);
|
||||
inputs.add(randomstring);
|
||||
inputs.add(randomstringErr);
|
||||
DatabaseType.addDefaultDBPars(inputs);
|
||||
}catch (Throwable e) {
|
||||
e.printStackTrace();
|
||||
AnalysisLogger.getLogger().debug(e.toString());
|
||||
}
|
||||
call=true;
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public StatisticalType getOutput() {
|
||||
|
||||
List<TableTemplates> outtemplate = new ArrayList<TableTemplates>();
|
||||
outtemplate.add(TableTemplates.GENERIC);
|
||||
List<TableTemplates> outtemplateErr = new ArrayList<TableTemplates>();
|
||||
outtemplateErr.add(TableTemplates.GENERIC);
|
||||
|
||||
// OutputTable out = new OutputTable(outtemplate, outputtablename,
|
||||
// outputtable, "The output table containing all the matches");
|
||||
OutputTable outErr = new OutputTable(outtemplate, outputErrortablename,
|
||||
tableError, "The output table containing all the matches");
|
||||
PrimitiveType f = new PrimitiveType(File.class.getName(), new File(
|
||||
fileName), PrimitiveTypes.FILE, "OccFile", "OccFile");
|
||||
map.put("Output", f);
|
||||
// map.put("Output", out);
|
||||
map.put("Errors", outErr);
|
||||
PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map,
|
||||
PrimitiveTypes.MAP, "ResultsMap", "Results Map");
|
||||
|
||||
return output;
|
||||
// return out;
|
||||
|
||||
}
|
||||
|
||||
public void write(String writeSt) {
|
||||
try {
|
||||
out.write(writeSt);
|
||||
|
||||
} catch (IOException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
enum DataProvidersType {
|
||||
}
|
||||
|
||||
class DataPenum extends DynamicEnum {
|
||||
public Field[] getFields() {
|
||||
Field[] fields = DataProvidersType.class.getDeclaredFields();
|
||||
return fields;
|
||||
}
|
||||
}
|
||||
enum ExtentionDPType {
|
||||
}
|
||||
|
||||
class ExtentionDPEnum extends DynamicEnum {
|
||||
public Field[] getFields() {
|
||||
Field[] fields = ExtentionDPType.class.getDeclaredFields();
|
||||
return fields;
|
||||
}
|
||||
}
|
||||
enum UnfoldDPEnumType {
|
||||
}
|
||||
|
||||
class UnfoldDPEnum extends DynamicEnum {
|
||||
public Field[] getFields() {
|
||||
Field[] fields = UnfoldDPEnumType.class.getDeclaredFields();
|
||||
return fields;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,429 @@
|
|||
package org.gcube.dataanalysis.JobSMspd;
|
||||
|
||||
import static org.gcube.data.spd.client.plugins.AbstractPlugin.manager;
|
||||
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.File;
|
||||
import java.io.FileWriter;
|
||||
import java.io.IOException;
|
||||
import java.lang.reflect.Field;
|
||||
import java.sql.Connection;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.SQLException;
|
||||
import java.sql.Statement;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Map.Entry;
|
||||
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.data.spd.client.proxies.Manager;
|
||||
import org.gcube.data.spd.model.Conditions;
|
||||
import org.gcube.data.spd.model.PluginDescription;
|
||||
import org.gcube.data.spd.model.util.Capabilities;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.ColumnTypesList;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.OutputTable;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.ServiceType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.ServiceParameters;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
|
||||
import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory;
|
||||
import org.gcube.dataanalysis.ecoengine.utils.DatabaseUtils;
|
||||
import org.gcube.dataanalysis.ecoengine.utils.DynamicEnum;
|
||||
import org.hibernate.SessionFactory;
|
||||
|
||||
public class TaxaProcedure extends StandardLocalExternalAlgorithm {
|
||||
|
||||
LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
|
||||
static String databaseParameterName = "FishBase";
|
||||
static String userParameterName = "user";
|
||||
static String passwordParameterName = "password";
|
||||
static String urlParameterName = "FishBase";
|
||||
SessionFactory dbconnection = null;
|
||||
public static boolean call=false;
|
||||
String tablename;
|
||||
String columnnames;
|
||||
List<Object> speciesList;
|
||||
protected String fileName;
|
||||
BufferedWriter out;
|
||||
String outputtablename;
|
||||
String outputErrortablename;
|
||||
String outputtable;
|
||||
HashMap<String, String>dpHash= new HashMap<String, String>();
|
||||
HashMap<String, String>dpUHash= new HashMap<String, String>();
|
||||
HashMap<String, String>dpEHash= new HashMap<String, String>();
|
||||
String tableError;
|
||||
private DataPenum dp = new DataPenum();
|
||||
private ExtentionDPEnum dpE = new ExtentionDPEnum();
|
||||
private UnfoldDPEnum dpU = new UnfoldDPEnum();
|
||||
private String dataProvider = "Data Provider :";
|
||||
private String chosendataProvider = new String();
|
||||
private String dataProviderExtention = "Data Provider (Expand Option):";
|
||||
private String chosendataProviderExtention=new String();
|
||||
//private String chosendataProviderUnfold="Data Provider Unfold:";
|
||||
private String dataProviderUnfold = "Data Provider (Unfold Option):";
|
||||
private String chosendataProviderUnfold=new String();
|
||||
|
||||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "An algorithm that once data provider and search options are selecteced, it has to return the taxon";
|
||||
}
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
AnalysisLogger.getLogger().debug("SMFaoAlg");
|
||||
|
||||
}
|
||||
|
||||
public void fulfilParameters() throws IOException {
|
||||
config.setParam("DatabaseDriver", "org.postgresql.Driver");
|
||||
dbconnection = DatabaseUtils.initDBSession(config);
|
||||
tablename = getInputParameter("SpeciesTable");
|
||||
columnnames = getInputParameter("SpeciesColumns");
|
||||
|
||||
outputtablename = getInputParameter("OutputTableName");
|
||||
outputtable = getInputParameter("OutputTable");
|
||||
tableError = getInputParameter("ErrorTable");
|
||||
chosendataProviderUnfold = getInputParameter(dataProviderUnfold);
|
||||
chosendataProviderExtention = getInputParameter(dataProviderExtention);
|
||||
|
||||
chosendataProvider = getInputParameter(dataProvider);
|
||||
outputErrortablename = getInputParameter("ErrorTableName");
|
||||
|
||||
String[] columnlist = columnnames.split(AlgorithmConfiguration
|
||||
.getListSeparator());
|
||||
speciesList = DatabaseFactory.executeSQLQuery("select " + columnlist[0]
|
||||
+ " from " + tablename, dbconnection);
|
||||
fileName = super.config.getPersistencePath() + "results.csv";
|
||||
out = new BufferedWriter(new FileWriter(fileName));
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
protected void process() throws Exception {
|
||||
|
||||
try {
|
||||
fulfilParameters();
|
||||
createTables();
|
||||
|
||||
int lenght = (int) (speciesList.size() / 3);
|
||||
ArrayList<String> chunk1 = new ArrayList<String>();
|
||||
ArrayList<String> chunk2 = new ArrayList<String>();
|
||||
ArrayList<String> chunk3 = new ArrayList<String>();
|
||||
for (int i = 0; i < speciesList.size(); i++) {
|
||||
if (i < lenght)
|
||||
chunk1.add((String) speciesList.get(i));
|
||||
if (i >= lenght && i <= 2 * lenght)
|
||||
chunk2.add((String) speciesList.get(i));
|
||||
|
||||
if (i > 2 * lenght)
|
||||
|
||||
chunk3.add((String) speciesList.get(i));
|
||||
}
|
||||
|
||||
ThreadExtractionTaxaFromSPD t1 = new ThreadExtractionTaxaFromSPD(
|
||||
chunk1, chosendataProvider,chosendataProviderExtention,chosendataProviderUnfold);
|
||||
ThreadExtractionTaxaFromSPD t2 = new ThreadExtractionTaxaFromSPD(
|
||||
chunk2, chosendataProvider,chosendataProviderExtention,chosendataProviderUnfold);
|
||||
ThreadExtractionTaxaFromSPD t3 = new ThreadExtractionTaxaFromSPD(
|
||||
chunk3, chosendataProvider,chosendataProviderExtention,chosendataProviderUnfold);
|
||||
Thread th1 = new Thread(t1);
|
||||
th1.start();
|
||||
Thread th2 = new Thread(t2);
|
||||
th2.start();
|
||||
Thread th3 = new Thread(t3);
|
||||
th3.start();
|
||||
th1.join();
|
||||
th2.join();
|
||||
th3.join();
|
||||
write("scientific_name; author; citation; credits; id; lsid; providere; rank; ");
|
||||
out.newLine();
|
||||
insertInTheTable(t1.getInfo());
|
||||
insertInTheTable(t2.getInfo());
|
||||
insertInTheTable(t3.getInfo());
|
||||
|
||||
insertInTheTableErrors(t1.getErrors());
|
||||
insertInTheTableErrors(t2.getErrors());
|
||||
insertInTheTableErrors(t3.getErrors());
|
||||
|
||||
} catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
throw e;
|
||||
} finally {
|
||||
DatabaseUtils.closeDBConnection(dbconnection);
|
||||
out.close();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private void createTables() throws Exception {
|
||||
|
||||
|
||||
DatabaseFactory.executeSQLUpdate("create table " + tableError
|
||||
+ " (error character varying)", dbconnection);
|
||||
}
|
||||
|
||||
private void insertInTheTable(ArrayList<ArrayList<String>> arrays) throws IOException{
|
||||
|
||||
for (ArrayList<String> array : arrays) {
|
||||
// String query = "insert into " + outputtable + st + " values (";
|
||||
String writeString = new String();
|
||||
int i = 0;
|
||||
|
||||
for (String s : array) {
|
||||
if (i != 0) {
|
||||
writeString = writeString + "; ";
|
||||
}
|
||||
// query = query + ", ";}
|
||||
writeString = writeString + " '";
|
||||
// query = query + " '";
|
||||
if (s != null)
|
||||
s = s.replace("'", "");
|
||||
writeString = writeString + s;
|
||||
// query = query + s;
|
||||
// query = query + "'";
|
||||
writeString = writeString + "'";
|
||||
i++;
|
||||
|
||||
}
|
||||
write(writeString);
|
||||
out.newLine();
|
||||
// query = query + ")";
|
||||
// /* DatabaseFactory.executeSQLUpdate(query, dbconnection);*/
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private void insertInTheTableErrors(ArrayList<String> arrays)
|
||||
throws Exception {
|
||||
if (arrays != null) {
|
||||
String st = " (error)";
|
||||
for (String er : arrays) {
|
||||
String query = "insert into " + tableError + st + " values ('"
|
||||
+ er + "')";
|
||||
AnalysisLogger.getLogger().debug("query error : " + query);
|
||||
DatabaseFactory.executeSQLUpdate(query, dbconnection);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public void print(ArrayList<ArrayList<String>> arrays) {
|
||||
for (ArrayList<String> array : arrays) {
|
||||
|
||||
for (String s : array) {
|
||||
AnalysisLogger.getLogger().debug(s);
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
|
||||
}
|
||||
public void setDynamicParameter() {
|
||||
AnalysisLogger.getLogger().debug("Inside setDynamicParameter");
|
||||
ScopeProvider.instance.set("/gcube/devsec");
|
||||
Manager manager = null;
|
||||
|
||||
manager = manager().build();
|
||||
AnalysisLogger.getLogger().debug("costruito manager");
|
||||
AnalysisLogger.getLogger().debug("prima dei plugin");
|
||||
List<PluginDescription> plugin = manager.getPluginsDescription();
|
||||
AnalysisLogger.getLogger().debug("preso i plugin");
|
||||
|
||||
|
||||
dp.addEnum(DataProvidersType.class, "ALL");
|
||||
dpE.addEnum(ExtentionDPType.class, "ALL");
|
||||
dpU.addEnum(UnfoldDPEnumType.class, "NO OPTION");
|
||||
dpE.addEnum(ExtentionDPType.class, "NO OPTION");
|
||||
|
||||
|
||||
if (plugin != null) {
|
||||
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"*****PluginDescription is NOT null - length: "
|
||||
+ plugin.size());
|
||||
|
||||
for (int i = 0; i < plugin.size(); i++) {
|
||||
|
||||
PluginDescription pluginDescription = plugin.get(i);
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"For plugin ***"+pluginDescription.getName() );
|
||||
Map<Capabilities, List<Conditions>> pluginCapabilities = pluginDescription
|
||||
.getSupportedCapabilities();
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"created maps");
|
||||
AnalysisLogger.getLogger().debug(
|
||||
" map size"+pluginCapabilities.size());
|
||||
|
||||
for (Entry<Capabilities, List<Conditions>> pluginCapability : pluginCapabilities
|
||||
.entrySet()) {
|
||||
|
||||
Capabilities capability = pluginCapability.getKey();
|
||||
AnalysisLogger.getLogger().debug(
|
||||
capability.name().toString());
|
||||
if(capability.name().toString().equals("Unfold"))
|
||||
{
|
||||
|
||||
dpU.addEnum(UnfoldDPEnumType.class,pluginDescription.getName().toString() );
|
||||
}
|
||||
|
||||
if(capability.name().toString().equals("Expansion"))
|
||||
{
|
||||
|
||||
dpE.addEnum(ExtentionDPType.class,pluginDescription.getName().toString() );
|
||||
|
||||
}
|
||||
if(capability.name().toString().equals("Classification"))
|
||||
{
|
||||
dp.addEnum(DataProvidersType.class,pluginDescription.getName().toString());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
} else
|
||||
AnalysisLogger.getLogger().debug("*****PluginDescription is null");
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
try{
|
||||
AnalysisLogger.getLogger().debug("inside setInputParameters ");
|
||||
|
||||
addRemoteDatabaseInput(databaseParameterName, urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
List<TableTemplates> templates = new ArrayList<TableTemplates>();
|
||||
templates.add(TableTemplates.GENERIC);
|
||||
InputTable tinput = new InputTable(templates, "SpeciesTable",
|
||||
"The table containing the species information");
|
||||
ColumnTypesList columns = new ColumnTypesList("SpeciesTable",
|
||||
"SpeciesColumns", "Select the columns for species name", false);
|
||||
addStringInput("OutputTableName", "The name of the output table",
|
||||
"occ_");
|
||||
addStringInput("ErrorTableName", "The name of the output table", "err_");
|
||||
ServiceType randomstring = new ServiceType(
|
||||
ServiceParameters.RANDOMSTRING, "OutputTable", "", "occ");
|
||||
ServiceType randomstringErr = new ServiceType(
|
||||
ServiceParameters.RANDOMSTRING, "ErrorTable", "", "err");
|
||||
|
||||
|
||||
AnalysisLogger.getLogger().debug("before setDynamicParameter() ");
|
||||
if(!call)
|
||||
setDynamicParameter();
|
||||
|
||||
// try {
|
||||
//// if (justcall == 0) {
|
||||
//// justcall = 1;
|
||||
//
|
||||
//// }
|
||||
// } catch (Throwable e) {
|
||||
// e.printStackTrace();
|
||||
// AnalysisLogger.getLogger().debug(e.toString());
|
||||
// }
|
||||
|
||||
addEnumerateInput(DataProvidersType.values(), dataProvider,
|
||||
"Choose Data Providere", "ALL");
|
||||
AnalysisLogger.getLogger().debug("Dopo DataProvidersType");
|
||||
addEnumerateInput(ExtentionDPType.values(),dataProviderExtention ,
|
||||
"Choose Expand Option Data Providere","ALL");
|
||||
AnalysisLogger.getLogger().debug("Dopo ExtentionDPType");
|
||||
addEnumerateInput(UnfoldDPEnumType.values(), dataProviderUnfold,
|
||||
"Choose Unfold Option Data Providere","ALL");
|
||||
AnalysisLogger.getLogger().debug("Dopo UnfoldDPEnumType");
|
||||
|
||||
|
||||
inputs.add(tinput);
|
||||
inputs.add(columns);
|
||||
inputs.add(randomstring);
|
||||
inputs.add(randomstringErr);
|
||||
DatabaseType.addDefaultDBPars(inputs);
|
||||
}catch (Throwable e) {
|
||||
e.printStackTrace();
|
||||
AnalysisLogger.getLogger().debug(e.toString());
|
||||
}
|
||||
call=true;
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public StatisticalType getOutput() {
|
||||
|
||||
List<TableTemplates> outtemplate = new ArrayList<TableTemplates>();
|
||||
outtemplate.add(TableTemplates.GENERIC);
|
||||
List<TableTemplates> outtemplateErr = new ArrayList<TableTemplates>();
|
||||
outtemplateErr.add(TableTemplates.GENERIC);
|
||||
|
||||
// OutputTable out = new OutputTable(outtemplate, outputtablename,
|
||||
// outputtable, "The output table containing all the matches");
|
||||
OutputTable outErr = new OutputTable(outtemplate, outputErrortablename,
|
||||
tableError, "The output table containing all the matches");
|
||||
PrimitiveType f = new PrimitiveType(File.class.getName(), new File(
|
||||
fileName), PrimitiveTypes.FILE, "OccFile", "OccFile");
|
||||
map.put("Output", f);
|
||||
// map.put("Output", out);
|
||||
map.put("Errors", outErr);
|
||||
PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map,
|
||||
PrimitiveTypes.MAP, "ResultsMap", "Results Map");
|
||||
|
||||
return output;
|
||||
// return out;
|
||||
|
||||
}
|
||||
|
||||
public void write(String writeSt) {
|
||||
try {
|
||||
out.write(writeSt);
|
||||
|
||||
} catch (IOException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
enum DataProvidersType {
|
||||
}
|
||||
|
||||
class DataPenum extends DynamicEnum {
|
||||
public Field[] getFields() {
|
||||
Field[] fields = DataProvidersType.class.getDeclaredFields();
|
||||
return fields;
|
||||
}
|
||||
}
|
||||
enum ExtentionDPType {
|
||||
}
|
||||
|
||||
class ExtentionDPEnum extends DynamicEnum {
|
||||
public Field[] getFields() {
|
||||
Field[] fields = ExtentionDPType.class.getDeclaredFields();
|
||||
return fields;
|
||||
}
|
||||
}
|
||||
enum UnfoldDPEnumType {
|
||||
}
|
||||
|
||||
class UnfoldDPEnum extends DynamicEnum {
|
||||
public Field[] getFields() {
|
||||
Field[] fields = UnfoldDPEnumType.class.getDeclaredFields();
|
||||
return fields;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,160 @@
|
|||
package org.gcube.dataanalysis.JobSMspd;
|
||||
|
||||
import static org.gcube.data.spd.client.plugins.AbstractPlugin.manager;
|
||||
|
||||
import java.util.ArrayList;
|
||||
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.data.spd.client.proxies.Manager;
|
||||
import org.gcube.data.spd.model.products.OccurrencePoint;
|
||||
import org.gcube.data.spd.model.products.ResultElement;
|
||||
|
||||
import org.gcube.data.streams.Stream;
|
||||
|
||||
public class ThreadExtractionOccFromSPD implements Runnable {
|
||||
private ArrayList<String> chunk;
|
||||
private ArrayList<ArrayList<String>> informations;
|
||||
private ArrayList<String> errors;
|
||||
|
||||
private String dataProvider;
|
||||
private String dataProviderUnfold;
|
||||
private String dataProviderExpand;
|
||||
|
||||
|
||||
public ThreadExtractionOccFromSPD(ArrayList<String> chunk, String dataProvider,String dataProviderExpand,String dataProviderUnfold ) {
|
||||
this.chunk = chunk;
|
||||
for (String species : chunk) {
|
||||
System.out.println(species);
|
||||
// AnalysisLogger.getLogger().debug(species);
|
||||
}
|
||||
this.dataProvider=dataProvider;
|
||||
this.dataProviderExpand= dataProviderExpand;
|
||||
this.dataProviderUnfold=dataProviderUnfold;
|
||||
informations = new ArrayList<ArrayList<String>>();
|
||||
errors= new ArrayList<String>();
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
public void run() {
|
||||
|
||||
ScopeProvider.instance.set("/gcube/devsec");
|
||||
Manager manager=null;
|
||||
try{
|
||||
manager = manager().build();
|
||||
|
||||
for (String species : chunk) {
|
||||
if (species != null) {
|
||||
String query = new String();
|
||||
// if(dataProviderExpand.equals("NO OPTION"))
|
||||
// query= "SEARCH BY SN '"+species + "' RETURN occurrence";
|
||||
// else
|
||||
// query= "SEARCH BY SN '"+species + "' EXPAND WITH CatalogueOfLife RETURN occurrence";
|
||||
// System.out.println(query);
|
||||
query=createQueryParameter(species);
|
||||
AnalysisLogger.getLogger().debug("QUERY *******: "+query);
|
||||
Stream<ResultElement> stream;
|
||||
try {
|
||||
|
||||
stream = manager.search(query);
|
||||
int i=0;
|
||||
while (stream.hasNext()) {
|
||||
i++;
|
||||
|
||||
OccurrencePoint ti = (OccurrencePoint) stream.next();
|
||||
informations.add(crateRowTable(ti));
|
||||
|
||||
}
|
||||
if(i==0)
|
||||
{
|
||||
errors.add(species+" not found.");
|
||||
}
|
||||
} catch (Exception e) {
|
||||
errors.add("Exception on "+species+" :"+ e.getMessage());
|
||||
e.printStackTrace();
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
}catch(Throwable e){
|
||||
e.printStackTrace();
|
||||
AnalysisLogger.getLogger().debug("An error occurred: "+e.getMessage());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private String createQueryParameter(String species)
|
||||
{
|
||||
String query= "SEARCH BY SN '"+species +"'";
|
||||
String where=new String();
|
||||
String expand=new String();
|
||||
String unfold=new String();
|
||||
if(dataProvider.equals("ALL"))
|
||||
where="";
|
||||
else
|
||||
where=" IN "+dataProvider;
|
||||
|
||||
if(dataProviderUnfold.equals("NO OPTION"))
|
||||
unfold="";
|
||||
else
|
||||
unfold=" UNFOLD WITH "+dataProviderUnfold;
|
||||
|
||||
query= query +unfold;
|
||||
|
||||
if(dataProviderExpand.equals("ALL"))
|
||||
expand="EXPAND";
|
||||
{if(dataProviderExpand.equals("NO OPTION"))
|
||||
expand="";
|
||||
else
|
||||
expand=" EXPAND WITH "+dataProviderExpand;
|
||||
}
|
||||
query= query+ expand;
|
||||
if(!expand.equals("")& !dataProviderExpand.equals("NO OPTION") )
|
||||
|
||||
|
||||
|
||||
|
||||
query=query+ where;
|
||||
query= query +" RETURN occurrence";
|
||||
return query;
|
||||
}
|
||||
|
||||
|
||||
|
||||
private ArrayList<String> crateRowTable(OccurrencePoint p)
|
||||
{
|
||||
ArrayList<String> infoOcc= new ArrayList<String>();
|
||||
infoOcc.add(p.getScientificName());
|
||||
infoOcc.add(p.getAuthor());
|
||||
infoOcc.add(p.getCatalogueNumber());
|
||||
infoOcc.add(p.getCitation());
|
||||
infoOcc.add(p.getCollectionCode());
|
||||
infoOcc.add(p.getCoordinateUncertaintyInMeters());
|
||||
infoOcc.add(p.getCountry());
|
||||
infoOcc.add(p.getCredits());
|
||||
infoOcc.add(p.getFamily());
|
||||
infoOcc.add(p.getId());
|
||||
infoOcc.add(p.getInstitutionCode());
|
||||
infoOcc.add(p.getKingdom());
|
||||
infoOcc.add(p.getLocality());
|
||||
infoOcc.add(p.getProvider());
|
||||
infoOcc.add((Double.toString(p.getDecimalLatitude())));
|
||||
infoOcc.add((Double.toString(p.getDecimalLongitude())));
|
||||
infoOcc.add((Double.toString(p.getMaxDepth())));
|
||||
infoOcc.add((Double.toString(p.getMinDepth())));
|
||||
return infoOcc;
|
||||
|
||||
}
|
||||
public ArrayList<ArrayList<String>> getInfo()
|
||||
{
|
||||
return informations;
|
||||
}
|
||||
public ArrayList<String> getErrors()
|
||||
{
|
||||
return errors;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,151 @@
|
|||
package org.gcube.dataanalysis.JobSMspd;
|
||||
|
||||
import static org.gcube.data.spd.client.plugins.AbstractPlugin.manager;
|
||||
|
||||
import java.util.ArrayList;
|
||||
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.data.spd.client.proxies.Manager;
|
||||
import org.gcube.data.spd.model.products.OccurrencePoint;
|
||||
import org.gcube.data.spd.model.products.ResultElement;
|
||||
import org.gcube.data.spd.model.products.TaxonomyItem;
|
||||
|
||||
import org.gcube.data.streams.Stream;
|
||||
|
||||
public class ThreadExtractionTaxaFromSPD implements Runnable {
|
||||
private ArrayList<String> chunk;
|
||||
private ArrayList<ArrayList<String>> informations;
|
||||
private ArrayList<String> errors;
|
||||
|
||||
private String dataProvider;
|
||||
private String dataProviderUnfold;
|
||||
private String dataProviderExpand;
|
||||
|
||||
|
||||
public ThreadExtractionTaxaFromSPD(ArrayList<String> chunk, String dataProvider,String dataProviderExpand,String dataProviderUnfold ) {
|
||||
this.chunk = chunk;
|
||||
for (String species : chunk) {
|
||||
System.out.println(species);
|
||||
// AnalysisLogger.getLogger().debug(species);
|
||||
}
|
||||
this.dataProvider=dataProvider;
|
||||
this.dataProviderExpand= dataProviderExpand;
|
||||
this.dataProviderUnfold=dataProviderUnfold;
|
||||
informations = new ArrayList<ArrayList<String>>();
|
||||
errors= new ArrayList<String>();
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
public void run() {
|
||||
|
||||
ScopeProvider.instance.set("/gcube/devsec");
|
||||
Manager manager=null;
|
||||
try{
|
||||
manager = manager().build();
|
||||
|
||||
for (String species : chunk) {
|
||||
if (species != null) {
|
||||
String query = new String();
|
||||
// if(dataProviderExpand.equals("NO OPTION"))
|
||||
// query= "SEARCH BY SN '"+species + "' RETURN occurrence";
|
||||
// else
|
||||
// query= "SEARCH BY SN '"+species + "' EXPAND WITH CatalogueOfLife RETURN occurrence";
|
||||
// System.out.println(query);
|
||||
query=createQueryParameter(species);
|
||||
AnalysisLogger.getLogger().debug("QUERY *******: "+query);
|
||||
Stream<ResultElement> stream;
|
||||
try {
|
||||
|
||||
stream = manager.search(query);
|
||||
int i=0;
|
||||
while (stream.hasNext()) {
|
||||
i++;
|
||||
TaxonomyItem ti = (TaxonomyItem) stream.next();
|
||||
informations.add(crateRowTable(ti));
|
||||
|
||||
}
|
||||
if(i==0)
|
||||
{
|
||||
errors.add(species+" not found.");
|
||||
}
|
||||
} catch (Exception e) {
|
||||
errors.add("Exception on "+species+" :"+ e.getMessage());
|
||||
e.printStackTrace();
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
}catch(Throwable e){
|
||||
e.printStackTrace();
|
||||
AnalysisLogger.getLogger().debug("An error occurred: "+e.getMessage());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private String createQueryParameter(String species)
|
||||
{
|
||||
String query= "SEARCH BY SN '"+species +"'";
|
||||
String where=new String();
|
||||
String expand=new String();
|
||||
String unfold=new String();
|
||||
if(dataProvider.equals("ALL"))
|
||||
where="";
|
||||
else
|
||||
where=" IN "+dataProvider;
|
||||
|
||||
if(dataProviderUnfold.equals("NO OPTION"))
|
||||
unfold="";
|
||||
else
|
||||
unfold=" UNFOLD WITH "+dataProviderUnfold;
|
||||
|
||||
query= query +unfold;
|
||||
|
||||
if(dataProviderExpand.equals("ALL"))
|
||||
expand="EXPAND";
|
||||
{if(dataProviderExpand.equals("NO OPTION"))
|
||||
expand="";
|
||||
else
|
||||
expand=" EXPAND WITH "+dataProviderExpand;
|
||||
}
|
||||
query= query+ expand;
|
||||
if(!expand.equals("")& !dataProviderExpand.equals("NO OPTION") )
|
||||
|
||||
|
||||
|
||||
|
||||
query=query+ where;
|
||||
query= query +" RETURN TAXON";
|
||||
return query;
|
||||
}
|
||||
|
||||
|
||||
|
||||
private ArrayList<String> crateRowTable(TaxonomyItem p)
|
||||
{
|
||||
ArrayList<String> infoOcc= new ArrayList<String>();
|
||||
infoOcc.add(p.getScientificName());
|
||||
infoOcc.add(p.getAuthor());
|
||||
infoOcc.add(p.getCitation());
|
||||
infoOcc.add(p.getCredits());
|
||||
infoOcc.add(p.getId());
|
||||
infoOcc.add(p.getLsid());
|
||||
infoOcc.add(p.getProvider());
|
||||
infoOcc.add(p.getRank());
|
||||
|
||||
return infoOcc;
|
||||
|
||||
}
|
||||
public ArrayList<ArrayList<String>> getInfo()
|
||||
{
|
||||
return informations;
|
||||
}
|
||||
public ArrayList<String> getErrors()
|
||||
{
|
||||
return errors;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,186 @@
|
|||
package org.gcube.dataanalysis.trendylyzeralgorithms;
|
||||
|
||||
import java.awt.Image;
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.File;
|
||||
import java.io.FileOutputStream;
|
||||
import java.io.FileWriter;
|
||||
import java.io.IOException;
|
||||
import java.io.ObjectOutputStream;
|
||||
import java.sql.Connection;
|
||||
import java.sql.DriverManager;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.SQLException;
|
||||
import java.sql.Statement;
|
||||
import java.util.HashMap;
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import org.gcube.contentmanagement.graphtools.data.conversions.ImageTools;
|
||||
import org.gcube.contentmanagement.graphtools.plotting.graphs.HistogramGraph;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
|
||||
import org.jfree.chart.JFreeChart;
|
||||
import org.jfree.data.category.DefaultCategoryDataset;
|
||||
import org.postgresql.Driver;
|
||||
|
||||
public class AbsoluteSpeciesBarChartsAlgorithm extends
|
||||
StandardLocalExternalAlgorithm {
|
||||
|
||||
LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
|
||||
static String databaseName = "DatabaseName";
|
||||
static String userParameterName = "DatabaseUserName";
|
||||
static String passwordParameterName = "DatabasePassword";
|
||||
static String urlParameterName = "DatabaseURL";
|
||||
protected String fileName;
|
||||
BufferedWriter out;
|
||||
private String firstSpeciesNumber = " SpeciesNumber :";
|
||||
private String yearStart = "Start year :";
|
||||
private String yearEnd = "End year :";
|
||||
private int speciesNumber;
|
||||
String databaseJdbc;
|
||||
String year_start;
|
||||
String year_end;
|
||||
String databaseUser;
|
||||
String databasePwd;
|
||||
private Connection connection = null;
|
||||
private DefaultCategoryDataset defaultcategorydataset;
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
AnalysisLogger.getLogger().debug("Initialization");
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "An algorithm producing a bar chart for the most observed species in a certain years range (with respect to the OBIS database)";
|
||||
}
|
||||
|
||||
public void fulfilParameters() {
|
||||
String tmp = getInputParameter(firstSpeciesNumber);
|
||||
speciesNumber = Integer.parseInt(tmp);
|
||||
databaseJdbc = getInputParameter(urlParameterName);
|
||||
year_start = getInputParameter(yearStart);
|
||||
year_end = getInputParameter(yearEnd);
|
||||
databaseUser = getInputParameter(userParameterName);
|
||||
databasePwd = getInputParameter(passwordParameterName);
|
||||
fileName = super.config.getPersistencePath() + "results.csv";
|
||||
}
|
||||
|
||||
private ResultSet performeQuery() throws SQLException {
|
||||
|
||||
connection = DriverManager.getConnection(databaseJdbc, databaseUser,
|
||||
databasePwd);
|
||||
Statement stmt = connection.createStatement();
|
||||
String query = "SELECT tname, sum(count)AS count FROM public.count_species_per_year WHERE year::integer >="
|
||||
+ year_start
|
||||
+ "AND year::integer <="
|
||||
+ year_end
|
||||
+ "GROUP BY tname ORDER BY count desc;";
|
||||
return stmt.executeQuery(query);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void process() throws Exception {
|
||||
defaultcategorydataset = new DefaultCategoryDataset();
|
||||
String driverName = "org.postgresql.Driver";
|
||||
Class driverClass = Class.forName(driverName);
|
||||
Driver driver = (Driver) driverClass.newInstance();
|
||||
fulfilParameters();
|
||||
out = new BufferedWriter(new FileWriter(fileName));
|
||||
|
||||
ResultSet rs = performeQuery();
|
||||
int i = 0;
|
||||
String s = "Species";
|
||||
while (rs.next() && i < speciesNumber) {
|
||||
String tname = rs.getString("tname");
|
||||
String count = rs.getString("count");
|
||||
write(tname+","+count);
|
||||
int countOcc = Integer.parseInt(count);
|
||||
PrimitiveType val = new PrimitiveType(String.class.getName(),
|
||||
count, PrimitiveTypes.STRING, tname, tname);
|
||||
if(i<100)
|
||||
map.put(tname, val);
|
||||
if (i < 16)
|
||||
defaultcategorydataset.addValue(countOcc, s, tname);
|
||||
i++;
|
||||
|
||||
}
|
||||
out.close();
|
||||
connection.close();
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
addStringInput(
|
||||
firstSpeciesNumber,
|
||||
"Number of species to report (max 17 will be visualized on the chart)",
|
||||
"10");
|
||||
addStringInput(yearStart, "Starting year of the analysis", "1800");
|
||||
addStringInput(yearEnd, "Ending year of the analysis", "2020");
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
AnalysisLogger.getLogger().debug("Shutdown");
|
||||
}
|
||||
|
||||
@Override
|
||||
public StatisticalType getOutput() {
|
||||
PrimitiveType p = new PrimitiveType(Map.class.getName(),
|
||||
PrimitiveType.stringMap2StatisticalMap(outputParameters),
|
||||
PrimitiveTypes.MAP, "Discrepancy Analysis", "");
|
||||
AnalysisLogger
|
||||
.getLogger()
|
||||
.debug("MapsComparator: Producing Gaussian Distribution for the errors");
|
||||
// build image:
|
||||
HashMap<String, Image> producedImages = new HashMap<String, Image>();
|
||||
|
||||
JFreeChart chart = HistogramGraph
|
||||
.createStaticChart(defaultcategorydataset);
|
||||
Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
|
||||
|
||||
producedImages.put("Species Observations", image);
|
||||
|
||||
PrimitiveType images = new PrimitiveType(HashMap.class.getName(),
|
||||
producedImages, PrimitiveTypes.IMAGES, "ErrorRepresentation",
|
||||
"Graphical representation of the error spread");
|
||||
// PrimitiveType images = new PrimitiveType("Species Observations",
|
||||
// producedImages, PrimitiveTypes.IMAGES, "ErrorRepresentation",
|
||||
// "Graphical representation of the error spread");
|
||||
PrimitiveType f = new PrimitiveType(File.class.getName(), new File(
|
||||
fileName), PrimitiveTypes.FILE, "OccFile", "OccFile");
|
||||
// end build image
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"Bar Charts Species Occurrences Produced");
|
||||
// collect all the outputs
|
||||
map.put("File", f);
|
||||
map.put("Result", p);
|
||||
map.put("Images", images);
|
||||
|
||||
// generate a primitive type for the collection
|
||||
PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map,
|
||||
PrimitiveTypes.MAP, "ResultsMap", "Results Map");
|
||||
|
||||
return output;
|
||||
}
|
||||
|
||||
public void write(String writeSt) {
|
||||
try {
|
||||
out.write(writeSt);
|
||||
out.newLine();
|
||||
} catch (IOException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,6 @@
|
|||
package org.gcube.dataanalysis.trendylyzeralgorithms;
|
||||
|
||||
public enum AreaEnum {
|
||||
LME,
|
||||
MEOW
|
||||
}
|
||||
|
|
@ -0,0 +1,137 @@
|
|||
package org.gcube.dataanalysis.trendylyzeralgorithms;
|
||||
|
||||
import java.awt.Image;
|
||||
import java.sql.Connection;
|
||||
import java.sql.DriverManager;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.SQLException;
|
||||
import java.sql.Statement;
|
||||
import java.util.HashMap;
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import org.gcube.contentmanagement.graphtools.data.conversions.ImageTools;
|
||||
import org.gcube.contentmanagement.graphtools.plotting.graphs.HistogramGraph;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
|
||||
import org.jfree.chart.JFreeChart;
|
||||
import org.jfree.data.category.DefaultCategoryDataset;
|
||||
import org.postgresql.Driver;
|
||||
|
||||
public class SimpleAlgorithm extends StandardLocalExternalAlgorithm{
|
||||
|
||||
//case of db used
|
||||
static String urlParameterName = "DatabaseURL";
|
||||
static String userParameterName = "DatabaseUserName";
|
||||
static String passwordParameterName = "DatabasePassword";
|
||||
Class driverClass ;
|
||||
Driver driver ;
|
||||
Connection connection = null;
|
||||
|
||||
LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
|
||||
private DefaultCategoryDataset defaultcategorydataset;
|
||||
|
||||
private String species="Species";
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
AnalysisLogger.getLogger().debug("Initialization");
|
||||
String driverName = "org.postgresql.Driver";
|
||||
driverClass = Class.forName(driverName);
|
||||
driver = (Driver) driverClass.newInstance();
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
// TODO Auto-generated method stub
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void process() throws Exception {
|
||||
String userSelectedSp = getInputParameter(species);
|
||||
|
||||
String databaseJdbc = getInputParameter(urlParameterName);
|
||||
String databaseUser = getInputParameter(userParameterName);
|
||||
String databasePwd = getInputParameter(passwordParameterName);
|
||||
|
||||
connection = DriverManager.getConnection(databaseJdbc, databaseUser,
|
||||
databasePwd);
|
||||
Statement stmt = connection.createStatement();
|
||||
String query = "SELECT numberOfObservation FROM public.count_species_per_year WHERE tname ="
|
||||
+ species;
|
||||
ResultSet rs = stmt.executeQuery(query);
|
||||
int i =0;
|
||||
String s = "Species";
|
||||
while (rs.next()) {
|
||||
|
||||
|
||||
String count = rs.getString("numberOfObservation");
|
||||
int countOcc=Integer.parseInt(count);
|
||||
PrimitiveType val = new PrimitiveType(String.class.getName(), count, PrimitiveTypes.STRING, species, species);
|
||||
map.put(species, val);
|
||||
if(i<16)
|
||||
defaultcategorydataset.addValue(countOcc,s,species);
|
||||
else
|
||||
break;
|
||||
i++;
|
||||
|
||||
}
|
||||
connection.close();
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
addStringInput(species, "Slected species", "Solea solea");
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
AnalysisLogger.getLogger().debug("Shutdown");
|
||||
try {
|
||||
connection.close();
|
||||
} catch (SQLException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
}
|
||||
@Override
|
||||
public StatisticalType getOutput() {
|
||||
PrimitiveType p = new PrimitiveType(Map.class.getName(), PrimitiveType.stringMap2StatisticalMap(outputParameters), PrimitiveTypes.MAP, "Discrepancy Analysis","");
|
||||
AnalysisLogger.getLogger().debug("MapsComparator: Producing Gaussian Distribution for the errors");
|
||||
//build image:
|
||||
HashMap<String, Image> producedImages = new HashMap<String, Image>();
|
||||
|
||||
JFreeChart chart = HistogramGraph.createStaticChart(defaultcategorydataset);
|
||||
Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
|
||||
producedImages.put("Species Observations", image);
|
||||
|
||||
PrimitiveType images = new PrimitiveType(HashMap.class.getName(), producedImages, PrimitiveTypes.IMAGES, "ErrorRepresentation", "Graphical representation of the error spread");
|
||||
|
||||
//end build image
|
||||
AnalysisLogger.getLogger().debug("Bar Charts Species Occurrences Produced");
|
||||
//collect all the outputs
|
||||
|
||||
map.put("Result", p);
|
||||
map.put("Images", images);
|
||||
|
||||
//generate a primitive type for the collection
|
||||
PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map, PrimitiveTypes.MAP, "ResultsMap", "Results Map");
|
||||
|
||||
|
||||
return output;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,195 @@
|
|||
package org.gcube.dataanalysis.trendylyzeralgorithms;
|
||||
|
||||
import java.awt.Image;
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.File;
|
||||
import java.io.FileWriter;
|
||||
import java.io.IOException;
|
||||
import java.sql.Connection;
|
||||
import java.sql.DriverManager;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.SQLException;
|
||||
import java.sql.Statement;
|
||||
import java.util.HashMap;
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import org.gcube.contentmanagement.graphtools.data.conversions.ImageTools;
|
||||
import org.gcube.contentmanagement.graphtools.plotting.graphs.HistogramGraph;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
|
||||
import org.jfree.chart.JFreeChart;
|
||||
import org.jfree.data.category.DefaultCategoryDataset;
|
||||
import org.postgresql.Driver;
|
||||
|
||||
public class SpeciesObservationsAreaBarChart extends
|
||||
StandardLocalExternalAlgorithm {
|
||||
static String databaseName = "DatabaseName";
|
||||
static String userParameterName = "DatabaseUserName";
|
||||
static String passwordParameterName = "DatabasePassword";
|
||||
static String urlParameterName = "DatabaseURL";
|
||||
private String species = "Species :";
|
||||
private String yearStart = "Start year :";
|
||||
private String yearEnd = "End year :";
|
||||
private String area = "Area :";
|
||||
private String selectedSpecies;
|
||||
private DefaultCategoryDataset defaultcategorydataset;
|
||||
private LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
|
||||
String databaseJdbc;
|
||||
|
||||
|
||||
String year_start;
|
||||
String year_end ;
|
||||
String databaseUser ;
|
||||
String chosenArea ;
|
||||
String databasePwd ;
|
||||
String table ;
|
||||
String areaName;
|
||||
Connection connection = null;
|
||||
protected String fileName;
|
||||
BufferedWriter out;
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"SpeciesObservationsAreaBarChart Initialization");
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "An algorithm producing a bar chart for the distribution of a species along a certain type of marine area (e.g. LME or MEOW)";
|
||||
}
|
||||
|
||||
|
||||
public void fulfilParameters() throws IOException {
|
||||
|
||||
databaseJdbc = getInputParameter(urlParameterName);
|
||||
year_start = getInputParameter(yearStart);
|
||||
year_end = getInputParameter(yearEnd);
|
||||
selectedSpecies = getInputParameter(species);
|
||||
databaseUser = getInputParameter(userParameterName);
|
||||
chosenArea = getInputParameter(area);
|
||||
databasePwd = getInputParameter(passwordParameterName);
|
||||
table = "count_species_per_lme_per_year";
|
||||
areaName = "lme_name";
|
||||
if (chosenArea.equals("LME")) {
|
||||
table = "count_species_per_lme_per_year";
|
||||
areaName = "lme_name";
|
||||
} else if (chosenArea.equals("MEOW")) {
|
||||
table = "count_species_per_meow_per_year";
|
||||
areaName = "ecoregion";
|
||||
}
|
||||
fileName = super.config.getPersistencePath() + "results.csv";
|
||||
out = new BufferedWriter(new FileWriter(fileName));
|
||||
|
||||
}
|
||||
|
||||
private ResultSet performeQuery() throws SQLException {
|
||||
connection = DriverManager.getConnection(databaseJdbc, databaseUser,
|
||||
databasePwd);
|
||||
Statement stmt = connection.createStatement();
|
||||
String query = "SELECT tname," + areaName
|
||||
+ " ,sum(count) AS count FROM " + table + " WHERE upper(tname) like upper('"
|
||||
+ selectedSpecies + "') AND year::integer >=" + year_start
|
||||
+ "AND year::integer <=" + year_end
|
||||
+ "GROUP BY tname ,"+areaName+" ORDER BY count desc;";
|
||||
return stmt.executeQuery(query);
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
protected void process() throws Exception {
|
||||
defaultcategorydataset = new DefaultCategoryDataset();
|
||||
String driverName = "org.postgresql.Driver";
|
||||
|
||||
Class driverClass = Class.forName(driverName);
|
||||
Driver driver = (Driver) driverClass.newInstance();
|
||||
fulfilParameters() ;
|
||||
ResultSet rs = performeQuery() ;
|
||||
|
||||
String s = selectedSpecies;
|
||||
while (rs.next()) {
|
||||
String ar = rs.getString(areaName);
|
||||
String count = rs.getString("count");
|
||||
PrimitiveType val = new PrimitiveType(String.class.getName(), count, PrimitiveTypes.STRING, ar, ar);
|
||||
write(ar+","+count);
|
||||
map.put(ar, val);
|
||||
int countOcc = Integer.parseInt(count);
|
||||
|
||||
defaultcategorydataset.addValue(countOcc, s, ar);
|
||||
|
||||
}
|
||||
connection.close();
|
||||
out.close();
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
addStringInput(species, "The species to analyze", "");
|
||||
addEnumerateInput(AreaEnum.values(), area, "Choose the area type",
|
||||
AreaEnum.LME.name());
|
||||
addStringInput(yearStart, "Starting year of the analysis", "1800");
|
||||
addStringInput(yearEnd, " Ending year of the analysis", "2020");
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
AnalysisLogger.getLogger().debug("Shutdown");
|
||||
}
|
||||
|
||||
@Override
|
||||
public StatisticalType getOutput() {
|
||||
PrimitiveType p = new PrimitiveType(Map.class.getName(),
|
||||
PrimitiveType.stringMap2StatisticalMap(outputParameters),
|
||||
PrimitiveTypes.MAP, "", "");
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"MapsComparator: Producing Bar Chart for the errors");
|
||||
// build image:
|
||||
HashMap<String, Image> producedImages = new HashMap<String, Image>();
|
||||
|
||||
JFreeChart chart = HistogramGraph
|
||||
.createStaticChart(defaultcategorydataset);
|
||||
Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
|
||||
producedImages.put("Most observed species", image);
|
||||
|
||||
PrimitiveType images = new PrimitiveType(HashMap.class.getName(),
|
||||
producedImages, PrimitiveTypes.IMAGES, "Most observed species",
|
||||
"Most observed species");
|
||||
|
||||
// end build image
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"Bar Charts Species Occurrences Produced");
|
||||
// collect all the outputs
|
||||
PrimitiveType f = new PrimitiveType(File.class.getName(), new File(
|
||||
fileName), PrimitiveTypes.FILE, "Species observations per area", "ObsFile");
|
||||
map.put("Output",f);
|
||||
map.put("Result", p);
|
||||
map.put("Images", images);
|
||||
|
||||
// generate a primitive type for the collection
|
||||
PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map,
|
||||
PrimitiveTypes.MAP, "ResultsMap", "Results Map");
|
||||
|
||||
return output;
|
||||
}
|
||||
|
||||
public void write(String writeSt) {
|
||||
try {
|
||||
out.write(writeSt);
|
||||
out.newLine();
|
||||
} catch (IOException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,263 @@
|
|||
package org.gcube.dataanalysis.trendylyzeralgorithms;
|
||||
import java.awt.Image;
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.File;
|
||||
import java.io.FileWriter;
|
||||
import java.io.IOException;
|
||||
import java.lang.reflect.Field;
|
||||
import java.sql.Connection;
|
||||
import java.sql.DriverManager;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.SQLException;
|
||||
import java.sql.Statement;
|
||||
import java.util.HashMap;
|
||||
import java.util.Hashtable;
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import org.gcube.contentmanagement.graphtools.data.conversions.ImageTools;
|
||||
import org.gcube.contentmanagement.graphtools.plotting.graphs.TimeSeriesGraph;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveTypesList;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
|
||||
import org.gcube.dataanalysis.ecoengine.utils.DynamicEnum;
|
||||
import org.jfree.chart.JFreeChart;
|
||||
import org.jfree.data.time.TimeSeries;
|
||||
import org.jfree.data.time.TimeSeriesCollection;
|
||||
import org.jfree.data.time.Year;
|
||||
import org.postgresql.Driver;
|
||||
|
||||
|
||||
|
||||
|
||||
public class SpeciesObservationsPerLMEAreaPerYearLineChart extends StandardLocalExternalAlgorithm {
|
||||
|
||||
static String databaseName = "DatabaseName";
|
||||
static String userParameterName = "DatabaseUserName";
|
||||
static String passwordParameterName = "DatabasePassword";
|
||||
static String urlParameterName = "DatabaseURL";
|
||||
private String yearStart = "Start Year";
|
||||
private String yearEnd = "End Year";
|
||||
private Hashtable areaTable= new Hashtable<String , String>();
|
||||
private static String area = "AreaType";
|
||||
private String choseArea = "Area Name:";
|
||||
private String selectedAreaName;
|
||||
static int justcall=0;
|
||||
private String[] speciesNames;
|
||||
LMEenum enuArea=new LMEenum();
|
||||
private TimeSeriesCollection dataset;
|
||||
protected String fileName;
|
||||
BufferedWriter out;
|
||||
Connection connection = null;
|
||||
String year_start;
|
||||
String year_end ;
|
||||
String table = "count_species_per_lme_per_year";
|
||||
String areaName = "lme_name";
|
||||
|
||||
String databaseJdbc=new String() ;
|
||||
String databaseUser=new String() ;
|
||||
String databasePwd =new String();
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
if(justcall==0)
|
||||
{ justcall=1;
|
||||
|
||||
try {
|
||||
queryArea(getStaticConnection());
|
||||
} catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
addEnumerateInput(LMEenumType.values(), area, "Choose the area name",
|
||||
Util.formatAreaName("NORTH SEA"));
|
||||
//addStringInput(choseArea,"Choose the area name","");
|
||||
addStringInput(yearStart, "Starting year of the analysis", "1800");
|
||||
addStringInput(yearEnd, "Ending year of the analysis", "2020");
|
||||
PrimitiveTypesList speciesSelected = new PrimitiveTypesList(String.class.getName(),PrimitiveTypes.STRING, "Selected species", "List of the species to analyze", false);
|
||||
super.inputs.add(speciesSelected);
|
||||
|
||||
|
||||
|
||||
}
|
||||
//to do: change
|
||||
public void queryArea(Connection connection) throws SQLException
|
||||
{
|
||||
AnalysisLogger.getLogger().debug("call queryArea");
|
||||
String query= "select distinct(upper(lme_name)) as lme_name from geo.lme order by lme_name";
|
||||
Statement stmt = connection.createStatement();
|
||||
ResultSet rs = stmt.executeQuery(query);
|
||||
while (rs.next()) {
|
||||
|
||||
String area=rs.getString("lme_name");
|
||||
AnalysisLogger.getLogger().debug(area);
|
||||
//areaTable.put(Util.formatAreaName(area), area);
|
||||
enuArea.addEnum(LMEenumType.class, area);
|
||||
}
|
||||
connection.close();
|
||||
|
||||
|
||||
}
|
||||
|
||||
public Connection getStaticConnection() throws SQLException, ClassNotFoundException, InstantiationException, IllegalAccessException
|
||||
{
|
||||
Class.forName("org.postgresql.Driver");
|
||||
Connection connection = null;
|
||||
connection = DriverManager.getConnection(
|
||||
"jdbc:postgresql://obis2.i-marine.research-infrastructures.eu/obis","postgres", "0b1s@d4sc13nc3");
|
||||
|
||||
return connection;
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
// TODO Auto-generated method stub
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public StatisticalType getOutput() {
|
||||
PrimitiveType p = new PrimitiveType(Map.class.getName(),
|
||||
PrimitiveType.stringMap2StatisticalMap(outputParameters),
|
||||
PrimitiveTypes.MAP, "", "");
|
||||
AnalysisLogger
|
||||
.getLogger()
|
||||
.debug("MapsComparator: Producing Line Chart for the errors");
|
||||
// build image:
|
||||
HashMap<String, Image> producedImages = new HashMap<String, Image>();
|
||||
|
||||
JFreeChart chart = TimeSeriesGraph.createStaticChart(dataset, "yyyy");
|
||||
Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
|
||||
producedImages.put("Selected species observations per LME area("+ selectedAreaName+")", image);
|
||||
|
||||
PrimitiveType images = new PrimitiveType(HashMap.class.getName(),
|
||||
producedImages, PrimitiveTypes.IMAGES, "ErrorRepresentation",
|
||||
"Selected species observations per LME area ("+ selectedAreaName+")");
|
||||
|
||||
// end build image
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"Line Taxonomy Occurrences Produced");
|
||||
// collect all the outputs
|
||||
LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
|
||||
PrimitiveType f = new PrimitiveType(File.class.getName(), new File(
|
||||
fileName), PrimitiveTypes.FILE, "Species observations per area", "ObsFile");
|
||||
map.put("Output",f);
|
||||
map.put("Result", p);
|
||||
map.put("Images", images);
|
||||
|
||||
// generate a primitive type for the collection
|
||||
PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map,
|
||||
PrimitiveTypes.MAP, "ResultsMap", "Results Map");
|
||||
|
||||
return output;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"Initialization SpeciesObservationsPerAreaPerYearLineChart");
|
||||
|
||||
}
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "Algorithm returning most observed species in a specific years range (data collected from OBIS database).";
|
||||
|
||||
}
|
||||
public void fulfilParameters() throws IOException {
|
||||
dataset = new TimeSeriesCollection();
|
||||
|
||||
year_start = getInputParameter(yearStart);
|
||||
year_end = getInputParameter(yearEnd);
|
||||
table = "count_species_per_lme_per_year";
|
||||
areaName = "lme_name";
|
||||
selectedAreaName=getInputParameter(area);
|
||||
AnalysisLogger.getLogger().debug("*********NAMEE*******"+selectedAreaName);
|
||||
|
||||
databaseJdbc = getInputParameter(urlParameterName);
|
||||
databaseUser = getInputParameter(userParameterName);
|
||||
databasePwd = getInputParameter(passwordParameterName);
|
||||
|
||||
fileName = super.config.getPersistencePath() + "results.csv";
|
||||
out = new BufferedWriter(new FileWriter(fileName));
|
||||
|
||||
}
|
||||
@Override
|
||||
protected void process() throws Exception {
|
||||
AnalysisLogger.getLogger().debug("Starto to process");
|
||||
String driverName = "org.postgresql.Driver";
|
||||
Class driverClass = Class.forName(driverName);
|
||||
Driver driver = (Driver) driverClass.newInstance();
|
||||
fulfilParameters();
|
||||
connection = DriverManager.getConnection(databaseJdbc, databaseUser,
|
||||
databasePwd);
|
||||
Statement stmt = connection.createStatement();
|
||||
speciesNames = config.getParam("Selected species").split(AlgorithmConfiguration.getListSeparator());
|
||||
for (String spe : speciesNames) {
|
||||
String query = "select lme_name,year,count from "+table+" where upper(tname) like upper('"+
|
||||
spe+ "') and upper(lme_name) like '"+selectedAreaName+"' and year::integer >="
|
||||
+ year_start
|
||||
+ "AND year::integer <="
|
||||
+ year_end +" order by year;";
|
||||
AnalysisLogger.getLogger().debug(query);
|
||||
|
||||
ResultSet rs = stmt.executeQuery(query);
|
||||
|
||||
final TimeSeries series = new TimeSeries(spe);
|
||||
|
||||
while (rs.next()) {
|
||||
if (rs.getString("year") != null) {
|
||||
AnalysisLogger.getLogger().debug(rs.getString("year")+" count "+ rs.getString("count"));
|
||||
|
||||
int year = Integer.parseInt(rs.getString("year"));
|
||||
int count = Integer.parseInt(rs.getString("count"));
|
||||
write(spe+","+year+","+count);
|
||||
series.add(new Year(year), count);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
dataset.addSeries(series);
|
||||
|
||||
}
|
||||
AnalysisLogger.getLogger().debug(dataset.toString());
|
||||
|
||||
connection.close();
|
||||
out.close();
|
||||
|
||||
}
|
||||
enum LMEenumType {}
|
||||
|
||||
class LMEenum extends DynamicEnum{
|
||||
public Field[] getFields() {
|
||||
Field[] fields = LMEenumType.class.getDeclaredFields();
|
||||
return fields;
|
||||
}
|
||||
}
|
||||
public void write(String writeSt) {
|
||||
try {
|
||||
out.write(writeSt);
|
||||
out.newLine();
|
||||
} catch (IOException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,259 @@
|
|||
package org.gcube.dataanalysis.trendylyzeralgorithms;
|
||||
|
||||
import java.awt.Image;
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.File;
|
||||
import java.io.FileWriter;
|
||||
import java.io.IOException;
|
||||
import java.lang.reflect.Field;
|
||||
import java.sql.Connection;
|
||||
import java.sql.DriverManager;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.SQLException;
|
||||
import java.sql.Statement;
|
||||
import java.util.HashMap;
|
||||
import java.util.Hashtable;
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import org.gcube.contentmanagement.graphtools.data.conversions.ImageTools;
|
||||
import org.gcube.contentmanagement.graphtools.plotting.graphs.TimeSeriesGraph;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveTypesList;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
|
||||
import org.gcube.dataanalysis.ecoengine.utils.DynamicEnum;
|
||||
import org.jfree.chart.JFreeChart;
|
||||
import org.jfree.data.time.TimeSeries;
|
||||
import org.jfree.data.time.TimeSeriesCollection;
|
||||
import org.jfree.data.time.Year;
|
||||
import org.postgresql.Driver;
|
||||
|
||||
public class SpeciesObservationsPerMEOWAreaPerYearLineChart extends StandardLocalExternalAlgorithm {
|
||||
|
||||
static String databaseName = "DatabaseName";
|
||||
static String userParameterName = "DatabaseUserName";
|
||||
static String passwordParameterName = "DatabasePassword";
|
||||
static String urlParameterName = "DatabaseURL";
|
||||
private String yearStart = "Start Year";
|
||||
private String yearEnd = "End Year";
|
||||
private Hashtable areaTable= new Hashtable<String , String>();
|
||||
private static String area = "AreaType";
|
||||
private String choseArea = "Area Name:";
|
||||
private String selectedAreaName;
|
||||
static int justcall=0;
|
||||
private String[] speciesNames;
|
||||
MEOWenum enuArea=new MEOWenum();
|
||||
private TimeSeriesCollection dataset;
|
||||
protected String fileName;
|
||||
BufferedWriter out;
|
||||
Connection connection = null;
|
||||
String year_start ;
|
||||
String year_end ;
|
||||
String table = "count_species_per_meow_per_year";
|
||||
String areaName = "ecoregion";
|
||||
String databaseJdbc;
|
||||
String databaseUser ;
|
||||
String databasePwd;
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
if(justcall==0)
|
||||
{ justcall=1;
|
||||
|
||||
try {
|
||||
queryArea(getStaticConnection());
|
||||
} catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
addEnumerateInput(MEOWEnumType.values(), area, "Choose the area name",
|
||||
Util.formatAreaName("AGULHAS BANK"));
|
||||
|
||||
//addStringInput(choseArea,"Choose the area name","");
|
||||
addStringInput(yearStart, "Starting year of the analysis", "1800");
|
||||
addStringInput(yearEnd, "Ending year of the analysis", "2020");
|
||||
PrimitiveTypesList speciesSelected = new PrimitiveTypesList(String.class.getName(),PrimitiveTypes.STRING, "Selected species", "List of the species to analyze", false);
|
||||
super.inputs.add(speciesSelected);
|
||||
|
||||
|
||||
|
||||
}
|
||||
//to do: change
|
||||
public void queryArea(Connection connection) throws SQLException
|
||||
{
|
||||
AnalysisLogger.getLogger().debug("call queryArea");
|
||||
String query= "select upper(ecoregion)as ecoregion from geo.meow order by ecoregion";
|
||||
Statement stmt = connection.createStatement();
|
||||
ResultSet rs = stmt.executeQuery(query);
|
||||
while (rs.next()) {
|
||||
|
||||
String area=rs.getString("ecoregion");
|
||||
AnalysisLogger.getLogger().debug(area);
|
||||
//areaTable.put(Util.formatAreaName(area), area);
|
||||
enuArea.addEnum(MEOWEnumType.class, area);
|
||||
}
|
||||
connection.close();
|
||||
|
||||
|
||||
}
|
||||
|
||||
public Connection getStaticConnection() throws SQLException, ClassNotFoundException, InstantiationException, IllegalAccessException
|
||||
{
|
||||
Class.forName("org.postgresql.Driver");
|
||||
Connection connection = null;
|
||||
connection = DriverManager.getConnection(
|
||||
"jdbc:postgresql://obis2.i-marine.research-infrastructures.eu/obis","postgres", "0b1s@d4sc13nc3");
|
||||
|
||||
return connection;
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
// TODO Auto-generated method stub
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public StatisticalType getOutput() {
|
||||
PrimitiveType p = new PrimitiveType(Map.class.getName(),
|
||||
PrimitiveType.stringMap2StatisticalMap(outputParameters),
|
||||
PrimitiveTypes.MAP, "", "");
|
||||
AnalysisLogger
|
||||
.getLogger()
|
||||
.debug("MapsComparator: Producing Line Chart for the errors");
|
||||
// build image:
|
||||
HashMap<String, Image> producedImages = new HashMap<String, Image>();
|
||||
|
||||
JFreeChart chart = TimeSeriesGraph.createStaticChart(dataset, "yyyy");
|
||||
Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
|
||||
producedImages.put("Selected species observations per MEOW area ("+ selectedAreaName+")", image);
|
||||
|
||||
PrimitiveType images = new PrimitiveType(HashMap.class.getName(),
|
||||
producedImages, PrimitiveTypes.IMAGES, "ErrorRepresentation",
|
||||
"Selected species observations per MEOW area("+ selectedAreaName+")");
|
||||
|
||||
// end build image
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"Line Taxonomy Occurrences Produced");
|
||||
// collect all the outputs
|
||||
LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
|
||||
PrimitiveType f = new PrimitiveType(File.class.getName(), new File(
|
||||
fileName), PrimitiveTypes.FILE, "Species observations per area", "ObsFile");
|
||||
map.put("Output",f);
|
||||
map.put("Result", p);
|
||||
map.put("Images", images);
|
||||
|
||||
// generate a primitive type for the collection
|
||||
PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map,
|
||||
PrimitiveTypes.MAP, "ResultsMap", "Results Map");
|
||||
|
||||
return output;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"Initialization SpeciesObservationsPerAreaPerYearLineChart");
|
||||
|
||||
}
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "Algorithm returning most observed species in a specific years range (data collected from OBIS database).";
|
||||
|
||||
}
|
||||
public void fulfilParameters() throws Exception {
|
||||
String driverName = "org.postgresql.Driver";
|
||||
Class driverClass = Class.forName(driverName);
|
||||
Driver driver = (Driver) driverClass.newInstance();
|
||||
dataset = new TimeSeriesCollection();
|
||||
|
||||
year_start = getInputParameter(yearStart);
|
||||
year_end = getInputParameter(yearEnd);
|
||||
|
||||
selectedAreaName=getInputParameter(area);
|
||||
AnalysisLogger.getLogger().debug("*********NAMEE*******"+selectedAreaName);
|
||||
|
||||
databaseJdbc = getInputParameter(urlParameterName);
|
||||
databaseUser = getInputParameter(userParameterName);
|
||||
databasePwd = getInputParameter(passwordParameterName);
|
||||
connection = DriverManager.getConnection(databaseJdbc, databaseUser,
|
||||
databasePwd);
|
||||
fileName = super.config.getPersistencePath() + "results.csv";
|
||||
out = new BufferedWriter(new FileWriter(fileName));
|
||||
}
|
||||
@Override
|
||||
protected void process() throws Exception {
|
||||
AnalysisLogger.getLogger().debug("Start to process");
|
||||
fulfilParameters();
|
||||
|
||||
Statement stmt = connection.createStatement();
|
||||
speciesNames = config.getParam("Selected species").split(AlgorithmConfiguration.getListSeparator());
|
||||
for (String spe : speciesNames) {
|
||||
String query = "select ecoregion ,year,count from "+table+" where upper(tname) like upper('"+
|
||||
spe+ "') and upper(ecoregion) like '"+selectedAreaName+"' and year::integer >="
|
||||
+ year_start
|
||||
+ "AND year::integer <="
|
||||
+ year_end +" order by year;";
|
||||
AnalysisLogger.getLogger().debug(query);
|
||||
|
||||
ResultSet rs = stmt.executeQuery(query);
|
||||
|
||||
final TimeSeries series = new TimeSeries(spe);
|
||||
|
||||
while (rs.next()) {
|
||||
if (rs.getString("year") != null) {
|
||||
AnalysisLogger.getLogger().debug(rs.getString("year")+" count "+ rs.getString("count"));
|
||||
int year = Integer.parseInt(rs.getString("year"));
|
||||
int count = Integer.parseInt(rs.getString("count"));
|
||||
write(spe+","+year+","+count);
|
||||
series.add(new Year(year), count);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
dataset.addSeries(series);
|
||||
|
||||
}
|
||||
AnalysisLogger.getLogger().debug(dataset.toString());
|
||||
|
||||
connection.close();
|
||||
out.close();
|
||||
|
||||
}
|
||||
enum MEOWEnumType {}
|
||||
class MEOWenum extends DynamicEnum{
|
||||
public Field[] getFields() {
|
||||
|
||||
Field[] fields = MEOWEnumType.class.getDeclaredFields();
|
||||
return fields;
|
||||
}}
|
||||
public void write(String writeSt) {
|
||||
try {
|
||||
out.write(writeSt);
|
||||
out.newLine();
|
||||
} catch (IOException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,171 @@
|
|||
package org.gcube.dataanalysis.trendylyzeralgorithms;
|
||||
|
||||
import java.awt.Image;
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.File;
|
||||
import java.io.FileWriter;
|
||||
import java.sql.Connection;
|
||||
import java.sql.DriverManager;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.Statement;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import org.gcube.contentmanagement.graphtools.data.conversions.ImageTools;
|
||||
import org.gcube.contentmanagement.graphtools.plotting.graphs.HistogramGraph;
|
||||
import org.gcube.contentmanagement.graphtools.plotting.graphs.TimeSeriesGraph;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveTypesList;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
|
||||
import org.jfree.chart.JFreeChart;
|
||||
import org.jfree.chart.plot.ThermometerPlot;
|
||||
import org.jfree.data.category.DefaultCategoryDataset;
|
||||
import org.jfree.data.time.Minute;
|
||||
import org.jfree.data.time.TimeSeries;
|
||||
import org.jfree.data.time.TimeSeriesCollection;
|
||||
import org.jfree.data.time.Year;
|
||||
import org.postgresql.Driver;
|
||||
|
||||
public class SpeciesObservationsPerYear extends StandardLocalExternalAlgorithm {
|
||||
static String databaseName = "DatabaseName";
|
||||
static String userParameterName = "DatabaseUserName";
|
||||
static String passwordParameterName = "DatabasePassword";
|
||||
static String urlParameterName = "DatabaseURL";
|
||||
private String yearStart = "Start Year :";
|
||||
private String yearEnd = "End Year :";
|
||||
private String[] speciesNames;
|
||||
private TimeSeriesCollection dataset;
|
||||
protected String fileName;
|
||||
BufferedWriter out;
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"Initialization SpeciesObservationsPerYear");
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "An algorithm producing the trend of the observations for a certain species in a certain years range.";
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void process() throws Exception {
|
||||
dataset = new TimeSeriesCollection();
|
||||
String driverName = "org.postgresql.Driver";
|
||||
AnalysisLogger.getLogger().debug("Inside process ");
|
||||
fileName = super.config.getPersistencePath() + "results.csv";
|
||||
out = new BufferedWriter(new FileWriter(fileName));
|
||||
Class driverClass = Class.forName(driverName);
|
||||
Driver driver = (Driver) driverClass.newInstance();
|
||||
String databaseJdbc = getInputParameter(urlParameterName);
|
||||
String year_start = getInputParameter(yearStart);
|
||||
String year_end = getInputParameter(yearEnd);
|
||||
String databaseUser = getInputParameter(userParameterName);
|
||||
String databasePwd = getInputParameter(passwordParameterName);
|
||||
Connection connection = null;
|
||||
connection = DriverManager.getConnection(databaseJdbc, databaseUser,
|
||||
databasePwd);
|
||||
Statement stmt = connection.createStatement();
|
||||
|
||||
|
||||
|
||||
speciesNames = config.getParam("Selected species").split(AlgorithmConfiguration.getListSeparator());
|
||||
for (String sp : speciesNames) {
|
||||
AnalysisLogger.getLogger().debug("Species: " + sp);
|
||||
|
||||
String query = "select tname,year,count from public.count_species_per_year where upper(tname) like upper('"
|
||||
+ sp + "') and year::integer >"
|
||||
+ year_start
|
||||
+ "AND year::integer <"
|
||||
+ year_end +" order by year;";
|
||||
ResultSet rs = stmt.executeQuery(query);
|
||||
|
||||
final TimeSeries series = new TimeSeries(sp);
|
||||
|
||||
while (rs.next()) {
|
||||
if (rs.getString("year") != null) {
|
||||
|
||||
int year = Integer.parseInt(rs.getString("year"));
|
||||
int count = Integer.parseInt(rs.getString("count"));
|
||||
out.write(sp+","+year+","+count);
|
||||
out.newLine();
|
||||
|
||||
series.add(new Year(year), count);
|
||||
}
|
||||
}
|
||||
dataset.addSeries(series);
|
||||
|
||||
}
|
||||
AnalysisLogger.getLogger().debug(dataset.toString());
|
||||
out.close();
|
||||
connection.close();
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
public StatisticalType getOutput() {
|
||||
PrimitiveType p = new PrimitiveType(Map.class.getName(),
|
||||
PrimitiveType.stringMap2StatisticalMap(outputParameters),
|
||||
PrimitiveTypes.MAP, " ", "");
|
||||
AnalysisLogger
|
||||
.getLogger()
|
||||
.debug("MapsComparator: Producing Line Chart for the errors");
|
||||
// build image:
|
||||
HashMap<String, Image> producedImages = new HashMap<String, Image>();
|
||||
|
||||
JFreeChart chart = TimeSeriesGraph.createStaticChart(dataset, "yyyy");
|
||||
Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
|
||||
producedImages.put("Species observations per year", image);
|
||||
|
||||
PrimitiveType images = new PrimitiveType(HashMap.class.getName(),
|
||||
producedImages, PrimitiveTypes.IMAGES, "ErrorRepresentation",
|
||||
"Species observations per year");
|
||||
|
||||
// end build image
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"Line Species Occurrences Produced");
|
||||
// collect all the outputs
|
||||
LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
|
||||
PrimitiveType f = new PrimitiveType(File.class.getName(), new File(
|
||||
fileName), PrimitiveTypes.FILE, "Species observations per area", "ObsFile");
|
||||
map.put("Output",f);
|
||||
map.put("Result", p);
|
||||
map.put("Images", images);
|
||||
|
||||
// generate a primitive type for the collection
|
||||
PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map,
|
||||
PrimitiveTypes.MAP, "ResultsMap", "Results Map");
|
||||
|
||||
return output;
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
|
||||
addStringInput(yearStart, "Starting year of the analysis", "1800");
|
||||
addStringInput(yearEnd, "Ending year of the analysis", "2020");
|
||||
PrimitiveTypesList speciesSelected = new PrimitiveTypesList(String.class.getName(),PrimitiveTypes.STRING, "Selected species", "List of the species to analyze", false);
|
||||
super.inputs.add(speciesSelected);
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
// TODO Auto-generated method stub
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,9 @@
|
|||
package org.gcube.dataanalysis.trendylyzeralgorithms;
|
||||
|
||||
public enum TaxaEnum {
|
||||
GENUS,
|
||||
FAMILY,
|
||||
ORDER,
|
||||
CLASS
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,167 @@
|
|||
package org.gcube.dataanalysis.trendylyzeralgorithms;
|
||||
|
||||
import java.awt.Image;
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.File;
|
||||
import java.io.FileWriter;
|
||||
import java.sql.Connection;
|
||||
import java.sql.DriverManager;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.Statement;
|
||||
import java.util.HashMap;
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import org.gcube.contentmanagement.graphtools.data.conversions.ImageTools;
|
||||
import org.gcube.contentmanagement.graphtools.plotting.graphs.HistogramGraph;
|
||||
import org.gcube.contentmanagement.graphtools.plotting.graphs.TimeSeriesGraph;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
|
||||
import org.jfree.chart.JFreeChart;
|
||||
import org.jfree.data.category.DefaultCategoryDataset;
|
||||
import org.postgresql.Driver;
|
||||
|
||||
public class TaxaObservationsBarChartAlgorithm extends StandardLocalExternalAlgorithm{
|
||||
static String databaseName = "DatabaseName";
|
||||
static String userParameterName = "DatabaseUserName";
|
||||
static String passwordParameterName = "DatabasePassword";
|
||||
static String urlParameterName = "DatabaseURL";
|
||||
private String yearStart = "Start Year :";
|
||||
private String yearEnd = "End Year :";
|
||||
private String taxa = "Level :";
|
||||
String tax;
|
||||
protected String fileName;
|
||||
BufferedWriter out;
|
||||
private String firstTaxaNumber = "TaxaNumber :";
|
||||
private int taxaNumber;
|
||||
LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
|
||||
private DefaultCategoryDataset dataset;
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {AnalysisLogger.getLogger().debug(
|
||||
"Initialization TaxaObservationsBarChartAlgorithm");
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "An algorithm producing a bar chart for the most observed taxa in a certain years range (with respect to the OBIS database)";
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void process() throws Exception {
|
||||
dataset = new DefaultCategoryDataset();
|
||||
String driverName = "org.postgresql.Driver";
|
||||
String tmp=getInputParameter(firstTaxaNumber);
|
||||
|
||||
taxaNumber = Integer.parseInt(tmp);
|
||||
Class driverClass = Class.forName(driverName);
|
||||
Driver driver = (Driver) driverClass.newInstance();
|
||||
String databaseJdbc = getInputParameter(urlParameterName);
|
||||
String year_start = getInputParameter(yearStart);
|
||||
String year_end = getInputParameter(yearEnd);
|
||||
tax = getInputParameter(taxa);
|
||||
String databaseUser = getInputParameter(userParameterName);
|
||||
String databasePwd = getInputParameter(passwordParameterName);
|
||||
fileName = super.config.getPersistencePath() + "results.csv";
|
||||
out = new BufferedWriter(new FileWriter(fileName));
|
||||
Connection connection = null;
|
||||
connection = DriverManager.getConnection(databaseJdbc, databaseUser,
|
||||
databasePwd);
|
||||
String table="genus_table_per_year";
|
||||
String column_name="genus";
|
||||
if (tax.equals("LME")) {
|
||||
table = "genus_table_per_year";
|
||||
column_name = "genus";
|
||||
} else if (tax.equals("CLASS")) {
|
||||
table = "class_table_per_year";
|
||||
column_name = "class";
|
||||
} else if (tax.equals("FAMILY")) {
|
||||
table = "family_table_per_year";
|
||||
column_name = "family";
|
||||
} else if (tax.equals("ORDER")) {
|
||||
table = "order_table_per_year";
|
||||
column_name = "order";
|
||||
|
||||
}
|
||||
Statement stmt = connection.createStatement();
|
||||
String query = "SELECT \""+column_name+"\", sum(count)AS count FROM public."+ table+" WHERE year::integer >= "
|
||||
+ year_start
|
||||
+ "AND year::integer <= "
|
||||
+ year_end
|
||||
+ " GROUP BY \""+ column_name+"\" ORDER BY count desc;";
|
||||
ResultSet rs = stmt.executeQuery(query);
|
||||
int i =0;
|
||||
String s = column_name;
|
||||
while (rs.next()&& i<taxaNumber) {
|
||||
String tname = rs.getString(column_name);
|
||||
String count = rs.getString("count");
|
||||
out.write(column_name+","+count);
|
||||
out.newLine();
|
||||
if(i<100)
|
||||
{PrimitiveType val = new PrimitiveType(String.class.getName(), count, PrimitiveTypes.STRING, tname, tname);
|
||||
map.put(tname, val);}
|
||||
int countOcc=Integer.parseInt(count);
|
||||
if(i<16)
|
||||
dataset.addValue(countOcc,s,tname);
|
||||
|
||||
i++;
|
||||
|
||||
}
|
||||
connection.close();
|
||||
out.close();
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
addStringInput(firstTaxaNumber, "Number of taxa to report", "10");
|
||||
addEnumerateInput(TaxaEnum.values(), taxa, "Choose the taxonomy level",
|
||||
TaxaEnum.GENUS.name());
|
||||
addStringInput(yearStart, "Starting year of the analysis", "1800");
|
||||
addStringInput(yearEnd, "Ending year of the analysis", "2020");
|
||||
// addStringInput("Species", "The species", config.getParam("Species"));
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
// TODO Auto-generated method stub
|
||||
|
||||
}
|
||||
@Override
|
||||
public StatisticalType getOutput() {
|
||||
PrimitiveType p = new PrimitiveType(Map.class.getName(), PrimitiveType.stringMap2StatisticalMap(outputParameters), PrimitiveTypes.MAP, "Discrepancy Analysis","");
|
||||
AnalysisLogger.getLogger().debug("MapsComparator: Producing Gaussian Distribution for the errors");
|
||||
//build image:
|
||||
HashMap<String, Image> producedImages = new HashMap<String, Image>();
|
||||
|
||||
JFreeChart chart = HistogramGraph.createStaticChart(dataset);
|
||||
Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
|
||||
producedImages.put("Taxonomy observations per year ("+tax+")", image);
|
||||
|
||||
PrimitiveType images = new PrimitiveType(HashMap.class.getName(), producedImages, PrimitiveTypes.IMAGES, "ErrorRepresentation", "Graphical representation of the error spread");
|
||||
|
||||
//end build image
|
||||
AnalysisLogger.getLogger().debug("Line Charts Species Occurrences Produced");
|
||||
//collect all the outputs
|
||||
PrimitiveType f = new PrimitiveType(File.class.getName(), new File(
|
||||
fileName), PrimitiveTypes.FILE, "Species observations per area", "ObsFile");
|
||||
map.put("Output",f);
|
||||
map.put("Result", p);
|
||||
map.put("Images", images);
|
||||
|
||||
//generate a primitive type for the collection
|
||||
PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map, PrimitiveTypes.MAP, "ResultsMap", "Results Map");
|
||||
|
||||
|
||||
return output;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,198 @@
|
|||
package org.gcube.dataanalysis.trendylyzeralgorithms;
|
||||
|
||||
import java.awt.Image;
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.File;
|
||||
import java.io.FileWriter;
|
||||
import java.sql.Connection;
|
||||
import java.sql.DriverManager;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.Statement;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import org.gcube.contentmanagement.graphtools.data.conversions.ImageTools;
|
||||
import org.gcube.contentmanagement.graphtools.plotting.graphs.TimeSeriesGraph;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveTypesList;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
|
||||
import org.jfree.chart.JFreeChart;
|
||||
import org.jfree.data.time.TimeSeries;
|
||||
import org.jfree.data.time.TimeSeriesCollection;
|
||||
import org.jfree.data.time.Year;
|
||||
import org.postgresql.Driver;
|
||||
|
||||
public class TaxaObservationsPerYearLineChart
|
||||
extends StandardLocalExternalAlgorithm {
|
||||
static String databaseName = "DatabaseName";
|
||||
static String userParameterName = "DatabaseUserName";
|
||||
static String passwordParameterName = "DatabasePassword";
|
||||
static String urlParameterName = "DatabaseURL";
|
||||
private String yearStart = "Start year :";
|
||||
private String yearEnd = "End year :";
|
||||
private String taxa = "Level :";
|
||||
private String tax;
|
||||
|
||||
private String[] taxaNames;
|
||||
private TimeSeriesCollection dataset;
|
||||
protected String fileName;
|
||||
BufferedWriter out;
|
||||
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"Initialization TaxaObservationsPerYearLineChart");
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "Algorithm returning most observations taxonomy trend in a specific years range (with respect to the OBIS database)";
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
protected void process() throws Exception {
|
||||
String driverName = "org.postgresql.Driver";
|
||||
dataset = new TimeSeriesCollection();
|
||||
|
||||
Class driverClass = Class.forName(driverName);
|
||||
Driver driver = (Driver) driverClass.newInstance();
|
||||
String databaseJdbc = getInputParameter(urlParameterName);
|
||||
String year_start = getInputParameter(yearStart);
|
||||
String year_end = getInputParameter(yearEnd);
|
||||
fileName = super.config.getPersistencePath() + "results.csv";
|
||||
out = new BufferedWriter(new FileWriter(fileName));
|
||||
tax = getInputParameter(taxa);
|
||||
String table="genus_table_per_year";
|
||||
String column_name="genus";
|
||||
if (tax.equals("GENUS")) {
|
||||
table = "genus_table_per_year";
|
||||
column_name = "genus";
|
||||
} else if (tax.equals("CLASS")) {
|
||||
table = "class_table_per_year";
|
||||
column_name = "class";
|
||||
} else if (tax.equals("FAMILY")) {
|
||||
table = "family_table_per_year";
|
||||
column_name = "family";
|
||||
} else if (tax.equals("ORDER")) {
|
||||
table = "order_table_per_year";
|
||||
column_name = "order";
|
||||
|
||||
}
|
||||
|
||||
|
||||
// AnalysisLogger.getLogger().debug("Taxonomy found: " + taxonomy.size());
|
||||
|
||||
|
||||
String databaseUser = getInputParameter(userParameterName);
|
||||
String databasePwd = getInputParameter(passwordParameterName);
|
||||
Connection connection = null;
|
||||
connection = DriverManager.getConnection(databaseJdbc, databaseUser,
|
||||
databasePwd);
|
||||
Statement stmt = connection.createStatement();
|
||||
taxaNames = config.getParam("Selected taxonomy").split(AlgorithmConfiguration.getListSeparator());
|
||||
for (String tx : taxaNames) {
|
||||
AnalysisLogger.getLogger().debug("Species: " + tx);
|
||||
|
||||
String query = "select \""+ column_name+"\",year,count from "+table+" where upper("+column_name+") like upper('"
|
||||
+ tx + "') and year::integer >="
|
||||
+ year_start
|
||||
+ "AND year::integer <="
|
||||
+ year_end +" order by year;";
|
||||
AnalysisLogger.getLogger().debug(
|
||||
query);
|
||||
ResultSet rs = stmt.executeQuery(query);
|
||||
|
||||
final TimeSeries series = new TimeSeries(tx);
|
||||
|
||||
while (rs.next()) {
|
||||
if (rs.getString("year") != null) {
|
||||
|
||||
int year = Integer.parseInt(rs.getString("year"));
|
||||
int count = Integer.parseInt(rs.getString("count"));
|
||||
AnalysisLogger.getLogger().debug("year: " + year+ " count : "+ count);
|
||||
out.write(tx+","+year+","+count);
|
||||
out.newLine();
|
||||
series.add(new Year(year), count);
|
||||
}
|
||||
}
|
||||
dataset.addSeries(series);
|
||||
|
||||
}
|
||||
AnalysisLogger.getLogger().debug(dataset.toString());
|
||||
out.close();
|
||||
connection.close();
|
||||
}
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
addEnumerateInput(TaxaEnum.values(), taxa, "Choose the taxonomy level",
|
||||
TaxaEnum.GENUS.name());
|
||||
addStringInput(yearStart, "Starting year of the analysis", "1800");
|
||||
addStringInput(yearEnd, "Ending year of the analysis", "2020");
|
||||
PrimitiveTypesList taxaSelected = new PrimitiveTypesList(String.class.getName(),PrimitiveTypes.STRING, "Selected taxonomy", "List of taxa to analyze", false);
|
||||
super.inputs.add(taxaSelected);
|
||||
|
||||
// addStringInput("Species", "The species", config.getParam("Species"));
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
// TODO Auto-generated method stub
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public StatisticalType getOutput() {
|
||||
PrimitiveType p = new PrimitiveType(Map.class.getName(),
|
||||
PrimitiveType.stringMap2StatisticalMap(outputParameters),
|
||||
PrimitiveTypes.MAP, "Discrepancy Analysis", "");
|
||||
AnalysisLogger
|
||||
.getLogger()
|
||||
.debug("MapsComparator: Producing Line Chart for the errors");
|
||||
// build image:
|
||||
HashMap<String, Image> producedImages = new HashMap<String, Image>();
|
||||
|
||||
JFreeChart chart = TimeSeriesGraph.createStaticChart(dataset, "yyyy");
|
||||
Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
|
||||
producedImages.put("Taxa observations tends per year ("+tax+")", image);
|
||||
|
||||
PrimitiveType images = new PrimitiveType(HashMap.class.getName(),
|
||||
producedImages, PrimitiveTypes.IMAGES, "ErrorRepresentation",
|
||||
"Taxa observations per year ("+tax+")");
|
||||
|
||||
// end build image
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"Line Taxonomy Occurrences Produced");
|
||||
// collect all the outputs
|
||||
LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
|
||||
PrimitiveType f = new PrimitiveType(File.class.getName(), new File(
|
||||
fileName), PrimitiveTypes.FILE, "Species observations per area", "ObsFile");
|
||||
map.put("Output",f);
|
||||
map.put("Result", p);
|
||||
map.put("Images", images);
|
||||
|
||||
// generate a primitive type for the collection
|
||||
PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map,
|
||||
PrimitiveTypes.MAP, "ResultsMap", "Results Map");
|
||||
|
||||
return output;
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,63 @@
|
|||
package org.gcube.dataanalysis.trendylyzeralgorithms;
|
||||
import java.lang.reflect.Field;
|
||||
import java.sql.Connection;
|
||||
import java.sql.DriverManager;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.SQLException;
|
||||
import java.sql.Statement;
|
||||
import java.util.Hashtable;
|
||||
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.utils.DynamicEnum;
|
||||
import org.gcube.dataanalysis.trendylyzeralgorithms.Util;
|
||||
|
||||
|
||||
enum MEOWEnumType {}
|
||||
enum LMEenumType {}
|
||||
class MEOWenum {
|
||||
public Field[] getFields() {
|
||||
|
||||
Field[] fields = MEOWEnumType.class.getDeclaredFields();
|
||||
return fields;
|
||||
}}
|
||||
class LMEenum extends DynamicEnum{
|
||||
public Field[] getFields() {
|
||||
Field[] fields = LMEenumType.class.getDeclaredFields();
|
||||
return fields;
|
||||
}
|
||||
}
|
||||
public class Test {
|
||||
private static Hashtable<String, String> areaTable= new Hashtable<String , String>();
|
||||
private static LMEenum enuArea=new LMEenum();
|
||||
|
||||
public static void main(String [] args)
|
||||
{try {
|
||||
Connection connection = DriverManager.getConnection(
|
||||
"jdbc:postgresql://obis2.i-marine.research-infrastructures.eu/obis","postgres", "0b1s@d4sc13nc3");
|
||||
|
||||
AnalysisLogger.getLogger().debug("call queryArea");
|
||||
String query= "select upper(lme_name)as lme_name from geo.lme";
|
||||
Statement stmt;
|
||||
|
||||
stmt = connection.createStatement();
|
||||
|
||||
ResultSet rs = stmt.executeQuery(query);
|
||||
while (rs.next()) {
|
||||
|
||||
String area=rs.getString("lme_name");
|
||||
String formatArea=Util.formatAreaName(area);
|
||||
areaTable.put(formatArea, area);
|
||||
enuArea.addEnum(LMEenumType.class, Util.formatAreaName(area));
|
||||
LMEenumType selectEnumArea =LMEenumType.valueOf(Util.formatAreaName(area));
|
||||
String selectedAreaName=(String) areaTable.get(selectEnumArea.toString());
|
||||
System.out.print(selectedAreaName);
|
||||
System.out.println();
|
||||
}
|
||||
connection.close();
|
||||
}catch (Exception e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,15 @@
|
|||
package org.gcube.dataanalysis.trendylyzeralgorithms;
|
||||
|
||||
public class Util {
|
||||
|
||||
public static String formatAreaName(String area)
|
||||
{
|
||||
String temp= area.replace(".", "_");
|
||||
String temp2= temp.replace(" ", "_");
|
||||
temp= temp2.replace("-", "_");
|
||||
temp2= temp.replace(",", "_");
|
||||
temp= temp2.replace("/", "_");
|
||||
return temp;
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue