updated:
-trendylyzer algorithm to new obis db resource; -spd algorithm to new spd-model dependency version; git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineExternalAlgorithms@97277 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Angela Italiano
parent
5465a7f62f
commit
f6313e177e
10
.classpath
10
.classpath
|
|
@ -6,11 +6,6 @@
|
|||
<attribute name="maven.pomderived" value="true"/>
|
||||
</attributes>
|
||||
</classpathentry>
|
||||
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
|
||||
<attributes>
|
||||
<attribute name="maven.pomderived" value="true"/>
|
||||
</attributes>
|
||||
</classpathentry>
|
||||
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
|
||||
<attributes>
|
||||
<attribute name="maven.pomderived" value="true"/>
|
||||
|
|
@ -22,5 +17,10 @@
|
|||
<attribute name="maven.pomderived" value="true"/>
|
||||
</attributes>
|
||||
</classpathentry>
|
||||
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
|
||||
<attributes>
|
||||
<attribute name="maven.pomderived" value="true"/>
|
||||
</attributes>
|
||||
</classpathentry>
|
||||
<classpathentry kind="output" path="target/classes"/>
|
||||
</classpath>
|
||||
|
|
|
|||
|
|
@ -1,4 +1,3 @@
|
|||
#Tue Mar 19 10:56:09 CET 2013
|
||||
eclipse.preferences.version=1
|
||||
encoding//src/main/java=UTF-8
|
||||
encoding/<project>=UTF-8
|
||||
eclipse.preferences.version=1
|
||||
encoding//src/main/java=UTF-8
|
||||
encoding/<project>=UTF-8
|
||||
|
|
|
|||
|
|
@ -1,13 +1,12 @@
|
|||
#Tue Mar 19 10:56:09 CET 2013
|
||||
eclipse.preferences.version=1
|
||||
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
|
||||
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
|
||||
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
|
||||
org.eclipse.jdt.core.compiler.compliance=1.6
|
||||
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
|
||||
org.eclipse.jdt.core.compiler.debug.localVariable=generate
|
||||
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
|
||||
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
|
||||
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
|
||||
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
|
||||
org.eclipse.jdt.core.compiler.source=1.6
|
||||
eclipse.preferences.version=1
|
||||
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
|
||||
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
|
||||
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
|
||||
org.eclipse.jdt.core.compiler.compliance=1.7
|
||||
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
|
||||
org.eclipse.jdt.core.compiler.debug.localVariable=generate
|
||||
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
|
||||
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
|
||||
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
|
||||
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
|
||||
org.eclipse.jdt.core.compiler.source=1.7
|
||||
|
|
|
|||
64
pom.xml
64
pom.xml
|
|
@ -9,7 +9,7 @@
|
|||
</parent>
|
||||
<groupId>org.gcube.dataanalysis</groupId>
|
||||
<artifactId>ecological-engine-external-algorithms</artifactId>
|
||||
<version>1.1.1-SNAPSHOT</version>
|
||||
<version>1.1.3</version>
|
||||
<name>ecological-engine-external-algorithms</name>
|
||||
<description>ecological-engine-external-algorithms library</description>
|
||||
<properties>
|
||||
|
|
@ -19,7 +19,7 @@
|
|||
<dependency>
|
||||
<groupId>org.gcube.dataanalysis</groupId>
|
||||
<artifactId>ecological-engine</artifactId>
|
||||
<version>1.7.1-SNAPSHOT</version>
|
||||
<version>[1.0.0-SNAPSHOT, 3.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>rapidminer-custom</groupId>
|
||||
|
|
@ -31,6 +31,11 @@
|
|||
<artifactId>postgresql</artifactId>
|
||||
<version>8.4-702.jdbc4</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>rapidminer-custom</groupId>
|
||||
<artifactId>gsay-service</artifactId>
|
||||
<version>1.0.0</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.gcube.core</groupId>
|
||||
<artifactId>common-gcore-stubs</artifactId>
|
||||
|
|
@ -69,7 +74,6 @@
|
|||
<groupId>org.gcube.data.spd</groupId>
|
||||
<artifactId>spd-client-library</artifactId>
|
||||
<version>[3.0.0-SNAPSHOT, 4.0.0-SNAPSHOT)</version>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
<!-- This dependency is needed and is need on TOP to use GWT UI BInder
|
||||
without old Xerces version of gCore complaining -->
|
||||
|
|
@ -79,10 +83,6 @@
|
|||
<version>2.9.1</version>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
|
||||
|
||||
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.data.spd</groupId>
|
||||
<artifactId>spql-parser</artifactId>
|
||||
|
|
@ -93,53 +93,45 @@
|
|||
<dependency>
|
||||
<groupId>org.gcube.common</groupId>
|
||||
<artifactId>csv4j</artifactId>
|
||||
<version>[1.1.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
|
||||
<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.data.spd</groupId>
|
||||
<artifactId>spd-model</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT, 3.0.0-SNAPSHOT)</version>
|
||||
<!-- <version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version> -->
|
||||
<!-- UNCOMMENT THIS FOR RELEASE -->
|
||||
<scope>provided</scope>
|
||||
<version>[1.0.0-SNAPSHOT, 4.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.resources.discovery</groupId>
|
||||
<artifactId>discovery-client</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
|
||||
<scope>provided</scope>
|
||||
<groupId>org.gcube.resources.discovery</groupId>
|
||||
<artifactId>discovery-client</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.gcube.core</groupId>
|
||||
<artifactId>common-clients</artifactId>
|
||||
<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
|
||||
<groupId>org.gcube.core</groupId>
|
||||
<artifactId>common-clients</artifactId>
|
||||
<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.gcube.core</groupId>
|
||||
<artifactId>common-gcore-clients</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
|
||||
<groupId>org.gcube.core</groupId>
|
||||
<artifactId>common-gcore-clients</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
|
||||
|
||||
<!-- <dependency> -->
|
||||
<!-- <groupId>org.gcube.core</groupId> -->
|
||||
<!-- <artifactId>common-fw-clients</artifactId> -->
|
||||
<!-- <version>[1.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version> -->
|
||||
<!-- <scope>runtime</scope> -->
|
||||
<!-- </dependency> -->
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.resources.discovery</groupId>
|
||||
<artifactId>ic-client</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
|
||||
<groupId>org.gcube.resources.discovery</groupId>
|
||||
<artifactId>ic-client</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.core</groupId>
|
||||
<artifactId>common-scope-maps</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
|
||||
<groupId>org.gcube.core</groupId>
|
||||
<artifactId>common-scope-maps</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
|
||||
</dependencies>
|
||||
|
|
@ -155,8 +147,8 @@
|
|||
<plugin>
|
||||
<artifactId>maven-compiler-plugin</artifactId>
|
||||
<configuration>
|
||||
<source>1.6</source>
|
||||
<target>1.6</target>
|
||||
<source>1.7</source>
|
||||
<target>1.7</target>
|
||||
</configuration>
|
||||
</plugin>
|
||||
<plugin>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,19 @@
|
|||
package org.gcube.dataanalysis.JobSMspd;
|
||||
|
||||
public class Lock{
|
||||
|
||||
private boolean isLocked = false;
|
||||
|
||||
public synchronized void lock()
|
||||
throws InterruptedException{
|
||||
while(isLocked){
|
||||
wait();
|
||||
}
|
||||
isLocked = true;
|
||||
}
|
||||
|
||||
public synchronized void unlock(){
|
||||
isLocked = false;
|
||||
notify();
|
||||
}
|
||||
}
|
||||
|
|
@ -186,8 +186,8 @@ public class MapDwCA {
|
|||
file.write("\t");
|
||||
|
||||
//scientificNameAuthorship
|
||||
if (taxonomyItem.getAuthor()!= null)
|
||||
file.write(taxonomyItem.getAuthor());
|
||||
if (taxonomyItem.getScientificNameAuthorship()!= null)
|
||||
file.write(taxonomyItem.getScientificNameAuthorship());
|
||||
file.write("\t");
|
||||
|
||||
if (taxonomyItem.getCitation()!= null)
|
||||
|
|
|
|||
|
|
@ -2,17 +2,16 @@ package org.gcube.dataanalysis.JobSMspd;
|
|||
|
||||
import static org.gcube.data.spd.client.plugins.AbstractPlugin.manager;
|
||||
|
||||
import java.io.BufferedReader;
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.File;
|
||||
import java.io.FileInputStream;
|
||||
import java.io.FileWriter;
|
||||
import java.io.IOException;
|
||||
import java.io.InputStreamReader;
|
||||
import java.io.PrintWriter;
|
||||
import java.io.StringWriter;
|
||||
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;
|
||||
|
|
@ -26,9 +25,6 @@ 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.JobSMspd.TaxaProcedure.DataPenum;
|
||||
import org.gcube.dataanalysis.JobSMspd.TaxaProcedure.ExtentionDPEnum;
|
||||
import org.gcube.dataanalysis.JobSMspd.TaxaProcedure.UnfoldDPEnum;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.ColumnTypesList;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
|
||||
|
|
@ -56,10 +52,10 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
SessionFactory dbconnection = null;
|
||||
// public static boolean call=false;
|
||||
String tablename;
|
||||
File outputResult;
|
||||
String columnnames;
|
||||
List<Object> speciesList=null;
|
||||
List<Object> speciesList = null;
|
||||
protected String fileName;
|
||||
BufferedWriter out;
|
||||
String outputtablename;
|
||||
String outputErrortablename;
|
||||
String outputtable;
|
||||
|
|
@ -77,6 +73,7 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
// private String chosendataProviderUnfold="Data Provider Unfold:";
|
||||
private String dataProviderUnfold = "Data Provider (Unfold Option):";
|
||||
private String chosendataProviderUnfold = new String();
|
||||
private Lock lock = new Lock();
|
||||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
|
|
@ -86,6 +83,8 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
@Override
|
||||
public void init() throws Exception {
|
||||
AnalysisLogger.getLogger().debug("SMFaoAlg");
|
||||
AnalysisLogger.getLogger().debug("Init scope :"+ScopeProvider.instance.get());
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -109,7 +108,7 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
speciesList = DatabaseFactory.executeSQLQuery("select " + columnlist[0]
|
||||
+ " from " + tablename, dbconnection);
|
||||
fileName = super.config.getPersistencePath() + "results.csv";
|
||||
out = new BufferedWriter(new FileWriter(fileName));
|
||||
outputResult= new File(fileName);
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -118,6 +117,11 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
|
||||
try {
|
||||
String scope = ScopeProvider.instance.get();
|
||||
AnalysisLogger.getLogger().debug("process scope :"+scope);
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"-------Procedure config scope"
|
||||
+ config.getGcubeScope());
|
||||
|
||||
fulfilParameters();
|
||||
createTables();
|
||||
int lenght = (int) (speciesList.size() / 3);
|
||||
|
|
@ -152,13 +156,16 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
th1.join();
|
||||
th2.join();
|
||||
th3.join();
|
||||
write("scientific_name; author; catalogue_number; citation; collection_gode; cordinate_uncertaninty_in_meters; country;"
|
||||
+ "credits; family; id; institution_code; kingdom; locality; providere; latitude; longitude; max_depth; min_depth");
|
||||
out.newLine();
|
||||
|
||||
insertInTheTable(t1.getInfo());
|
||||
insertInTheTable(t2.getInfo());
|
||||
insertInTheTable(t3.getInfo());
|
||||
|
||||
|
||||
File []files= new File[3];
|
||||
if(t1.getInfo()!= null)
|
||||
files[0]=t1.getInfo();
|
||||
if(t1.getInfo()!= null)
|
||||
files[1]=t2.getInfo();
|
||||
if(t1.getInfo()!= null)
|
||||
files[2]=t3.getInfo();
|
||||
mergeFiles(files, outputResult);
|
||||
|
||||
insertInTheTableErrors(t1.getErrors());
|
||||
insertInTheTableErrors(t2.getErrors());
|
||||
|
|
@ -167,12 +174,12 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
} catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
AnalysisLogger.getLogger().debug(e.toString());
|
||||
|
||||
|
||||
throw e;
|
||||
} finally {
|
||||
|
||||
|
||||
DatabaseUtils.closeDBConnection(dbconnection);
|
||||
out.close();
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -183,33 +190,33 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
+ " (error character varying)", dbconnection);
|
||||
}
|
||||
|
||||
private void insertInTheTable(ArrayList<ArrayList<String>> arrays)
|
||||
throws Exception {
|
||||
|
||||
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 + "; ";
|
||||
}
|
||||
writeString = writeString + " '";
|
||||
if (s != null)
|
||||
s = s.replace("'", "");
|
||||
writeString = writeString + s;
|
||||
|
||||
writeString = writeString + "'";
|
||||
i++;
|
||||
|
||||
}
|
||||
write(writeString);
|
||||
out.newLine();
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
// private void insertInTheTable(ArrayList<ArrayList<String>> arrays)
|
||||
// throws Exception {
|
||||
//
|
||||
// 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 + "; ";
|
||||
// }
|
||||
// writeString = writeString + " '";
|
||||
// if (s != null)
|
||||
// s = s.replace("'", "");
|
||||
// writeString = writeString + s;
|
||||
//
|
||||
// writeString = writeString + "'";
|
||||
// i++;
|
||||
//
|
||||
// }
|
||||
// write(writeString);
|
||||
// out.newLine();
|
||||
//
|
||||
// }
|
||||
//
|
||||
// }
|
||||
|
||||
private void insertInTheTableErrors(ArrayList<String> arrays)
|
||||
throws Exception {
|
||||
|
|
@ -226,58 +233,79 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
}
|
||||
|
||||
private void insertEnumValuesr() {
|
||||
AnalysisLogger.getLogger().debug(" insertEnumValuesr");
|
||||
AnalysisLogger.getLogger().debug(" second version");
|
||||
if (dp == null || dpU == null || dpE == null) {
|
||||
dp = new DataPenum();
|
||||
dpE = new ExtentionDPEnum();
|
||||
dpU = new UnfoldDPEnum();
|
||||
setDynamicParameter();
|
||||
|
||||
try {
|
||||
setDynamicParameter();
|
||||
} catch (InterruptedException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
AnalysisLogger.getLogger().debug(" call setDynamicParameter");
|
||||
|
||||
}
|
||||
if (dp != null) {
|
||||
try {
|
||||
if (UnfoldDPEnumType.values().length == 0) {
|
||||
AnalysisLogger.getLogger().debug("Only one provider.");
|
||||
dp = new DataPenum();
|
||||
dpE = new ExtentionDPEnum();
|
||||
dpU = new UnfoldDPEnum();
|
||||
setDynamicParameter();
|
||||
}
|
||||
} catch (Exception e) {
|
||||
StringWriter sw = new StringWriter();
|
||||
PrintWriter pw = new PrintWriter(sw);
|
||||
e.printStackTrace(pw);
|
||||
AnalysisLogger.getLogger().debug(sw.toString());
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
AnalysisLogger.getLogger().debug("Shut down ");
|
||||
}
|
||||
|
||||
|
||||
|
||||
private void setDynamicParameter() {
|
||||
private void setDynamicParameter() throws InterruptedException {
|
||||
AnalysisLogger.getLogger().debug("Inside setDynamicParameter");
|
||||
// ScopeProvider.instance.set("/gcube/devsec");
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"Procedure called in the scope"
|
||||
"-------Procedure setParameter in the scope"
|
||||
+ ScopeProvider.instance.get().toString());
|
||||
|
||||
Manager manager = null;
|
||||
|
||||
manager = manager().build();
|
||||
AnalysisLogger.getLogger().debug("build Manager");
|
||||
AnalysisLogger.getLogger().debug("before dei plugin");
|
||||
List<PluginDescription> plugin=null;
|
||||
try{
|
||||
List<PluginDescription> plugin = null;
|
||||
try {
|
||||
plugin = manager.getPluginsDescription();
|
||||
}
|
||||
catch(Exception e)
|
||||
{
|
||||
String eTracMes= e.getMessage();
|
||||
} catch (Exception e) {
|
||||
String eTracMes = e.getMessage();
|
||||
StringWriter sw = new StringWriter();
|
||||
PrintWriter pw = new PrintWriter(sw);
|
||||
e.printStackTrace(pw);
|
||||
sw.toString();
|
||||
AnalysisLogger.getLogger().debug(eTracMes);
|
||||
AnalysisLogger.getLogger().debug(sw.toString());
|
||||
}
|
||||
finally
|
||||
{
|
||||
e.printStackTrace();
|
||||
} finally {
|
||||
lock.lock();
|
||||
dp.addEnum(DataProvidersType.class, "ALL");
|
||||
dpE.addEnum(ExtentionDPType.class, "ALL");
|
||||
dpU.addEnum(UnfoldDPEnumType.class, "NO OPTION");
|
||||
dpE.addEnum(ExtentionDPType.class, "NO OPTION");
|
||||
lock.unlock();
|
||||
}
|
||||
AnalysisLogger.getLogger().debug("get plugin");
|
||||
|
||||
|
||||
|
||||
if (plugin != null) {
|
||||
|
||||
AnalysisLogger.getLogger().debug(
|
||||
|
|
@ -297,9 +325,9 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
|
||||
for (Entry<Capabilities, List<Conditions>> pluginCapability : pluginCapabilities
|
||||
.entrySet()) {
|
||||
|
||||
|
||||
Capabilities capability = pluginCapability.getKey();
|
||||
String capabilityName=capability.name().toString();
|
||||
String capabilityName = capability.name().toString();
|
||||
AnalysisLogger.getLogger().debug(capabilityName);
|
||||
if (capabilityName.equals("Unfold"))
|
||||
dpU.addEnum(UnfoldDPEnumType.class, pluginDescription
|
||||
|
|
@ -347,11 +375,9 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
ServiceParameters.RANDOMSTRING, "OutputTable", "", "occ");
|
||||
ServiceType randomstringErr = new ServiceType(
|
||||
ServiceParameters.RANDOMSTRING, "ErrorTable", "", "err");
|
||||
|
||||
insertEnumValuesr();
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
addEnumerateInput(DataProvidersType.values(), dataProvider,
|
||||
"Choose Data Providere", "ALL");
|
||||
AnalysisLogger.getLogger().debug("After DataProvidersType");
|
||||
|
|
@ -361,7 +387,6 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
addEnumerateInput(UnfoldDPEnumType.values(), dataProviderUnfold,
|
||||
"Choose UnfoldRR Option Data Providere", "ALL");
|
||||
AnalysisLogger.getLogger().debug("After UnfoldDPEnumType");
|
||||
|
||||
inputs.add(tinput);
|
||||
inputs.add(columns);
|
||||
inputs.add(randomstring);
|
||||
|
|
@ -385,8 +410,7 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
|
||||
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");
|
||||
PrimitiveType f = new PrimitiveType(File.class.getName(), outputResult, PrimitiveTypes.FILE, "OccFile", "OccFile");
|
||||
map.put("Output", f);
|
||||
map.put("Errors", outErr);
|
||||
PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map,
|
||||
|
|
@ -396,17 +420,6 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
|
||||
}
|
||||
|
||||
public void write(String writeSt) {
|
||||
try {
|
||||
out.write(writeSt);
|
||||
|
||||
} catch (IOException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
enum DataProvidersType {
|
||||
}
|
||||
|
||||
|
|
@ -438,4 +451,57 @@ public class OccurencesProcedure extends StandardLocalExternalAlgorithm {
|
|||
}
|
||||
|
||||
}
|
||||
|
||||
public static void mergeFiles(File[] files, File mergedFile) {
|
||||
AnalysisLogger.getLogger().debug("Inside mergeFiles");
|
||||
if (mergedFile.exists()){
|
||||
mergedFile.delete();
|
||||
}
|
||||
FileWriter fstream = null;
|
||||
BufferedWriter out = null;
|
||||
try {
|
||||
fstream = new FileWriter(mergedFile, true);
|
||||
out = new BufferedWriter(fstream);
|
||||
} catch (IOException e1) {
|
||||
e1.printStackTrace();
|
||||
}
|
||||
String title = "institutionCode, " + "collectionCode, "
|
||||
+ "catalogueNumber, " + "dataSet, " + "dataProvider, "
|
||||
+ "dataSource, " + "scientificNameAuthorship,"
|
||||
+ "identifiedBy," + "credits," + "recordedBy, " + "eventDate, "
|
||||
+ "modified, " + "scientificName, " + "kingdom, " + "family, "
|
||||
+ "locality, " + "country, " + "citation, "
|
||||
+ "decimalLatitude, " + "decimalLongitude, "
|
||||
+ "coordinateUncertaintyInMeters, " + "maxDepth, "
|
||||
+ "minDepth, " + "basisOfRecord";
|
||||
try {
|
||||
out.write(title);
|
||||
out.newLine();
|
||||
for (File f : files) {
|
||||
System.out.println("merging: " + f.getName());
|
||||
FileInputStream fis;
|
||||
|
||||
fis = new FileInputStream(f);
|
||||
BufferedReader in = new BufferedReader(new InputStreamReader(
|
||||
fis));
|
||||
|
||||
String aLine;
|
||||
while ((aLine = in.readLine()) != null) {
|
||||
out.write(aLine);
|
||||
out.newLine();
|
||||
}
|
||||
|
||||
in.close();
|
||||
|
||||
}
|
||||
} catch (IOException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
try {
|
||||
out.close();
|
||||
} catch (IOException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -63,7 +63,7 @@ public class TaxaProcedure extends StandardLocalExternalAlgorithm {
|
|||
// public static boolean call=false;
|
||||
String tablename;
|
||||
String columnnames;
|
||||
List<Object> speciesList=null;
|
||||
List<Object> speciesList = null;
|
||||
// protected String fileName;
|
||||
// BufferedWriter out;
|
||||
String outputtablename;
|
||||
|
|
@ -73,8 +73,8 @@ public class TaxaProcedure extends StandardLocalExternalAlgorithm {
|
|||
HashMap<String, String> dpUHash = new HashMap<String, String>();
|
||||
HashMap<String, String> dpEHash = new HashMap<String, String>();
|
||||
String tableError;
|
||||
private static DataPenum dp = null;
|
||||
private static ExtentionDPEnum dpE = null;
|
||||
private static DataPenum dp = null;
|
||||
private static ExtentionDPEnum dpE = null;
|
||||
private static UnfoldDPEnum dpU = null;
|
||||
private String dataProvider = "Data Provider :";
|
||||
private String chosendataProvider = new String();
|
||||
|
|
@ -84,6 +84,8 @@ public class TaxaProcedure extends StandardLocalExternalAlgorithm {
|
|||
private String dataProviderUnfold = "Data Provider (Unfold Option):";
|
||||
private String chosendataProviderUnfold = new String();
|
||||
File file;
|
||||
private Lock lock = new Lock();
|
||||
|
||||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
|
|
@ -228,24 +230,43 @@ public class TaxaProcedure extends StandardLocalExternalAlgorithm {
|
|||
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
AnalysisLogger.getLogger().debug("Shut down ");
|
||||
}
|
||||
|
||||
private void insertEnumValuesr() {
|
||||
if (dp == null || dpU == null || dpE == null) {
|
||||
dp = new DataPenum();
|
||||
dpE = new ExtentionDPEnum();
|
||||
dpU = new UnfoldDPEnum();
|
||||
setDynamicParameter();
|
||||
}
|
||||
private void insertEnumValuesr() {
|
||||
AnalysisLogger.getLogger().debug(" insertEnumValuesr");
|
||||
|
||||
// if (dp == null || dpU == null || dpE == null) {
|
||||
// dp = new DataPenum();
|
||||
// dpE = new ExtentionDPEnum();
|
||||
// dpU = new UnfoldDPEnum();
|
||||
// AnalysisLogger.getLogger().debug(" call setDynamicParameter");
|
||||
//
|
||||
// setDynamicParameter();
|
||||
//
|
||||
// }
|
||||
// if (dp != null) {
|
||||
try {
|
||||
if (UnfoldDPEnumType.values().length == 0) {
|
||||
AnalysisLogger.getLogger().debug("Only one provider.");
|
||||
dp = new DataPenum();
|
||||
dpE = new ExtentionDPEnum();
|
||||
dpU = new UnfoldDPEnum();
|
||||
setDynamicParameter();
|
||||
}
|
||||
} catch (Exception e) {
|
||||
StringWriter sw = new StringWriter();
|
||||
PrintWriter pw = new PrintWriter(sw);
|
||||
e.printStackTrace(pw);
|
||||
AnalysisLogger.getLogger().debug(sw.toString());
|
||||
}
|
||||
// }
|
||||
|
||||
}
|
||||
|
||||
private void setDynamicParameter() {
|
||||
private void setDynamicParameter() {
|
||||
AnalysisLogger.getLogger().debug("Inside setDynamicParameter");
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"Procedure called in the scope"
|
||||
|
|
@ -259,18 +280,24 @@ public class TaxaProcedure extends StandardLocalExternalAlgorithm {
|
|||
try {
|
||||
plugin = manager.getPluginsDescription();
|
||||
} catch (Exception e) {
|
||||
String eTracMes= e.getMessage();
|
||||
String eTracMes = e.getMessage();
|
||||
StringWriter sw = new StringWriter();
|
||||
PrintWriter pw = new PrintWriter(sw);
|
||||
e.printStackTrace(pw);
|
||||
sw.toString();
|
||||
AnalysisLogger.getLogger().debug(eTracMes);
|
||||
AnalysisLogger.getLogger().debug(sw.toString());
|
||||
} finally {
|
||||
try {
|
||||
lock.lock();
|
||||
} catch (InterruptedException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
dp.addEnum(DataProvidersType.class, "ALL");
|
||||
dpE.addEnum(ExtentionDPType.class, "ALL");
|
||||
dpU.addEnum(UnfoldDPEnumType.class, "NO OPTION");
|
||||
dpE.addEnum(ExtentionDPType.class, "NO OPTION");
|
||||
lock.unlock();
|
||||
}
|
||||
AnalysisLogger.getLogger().debug("get plugin");
|
||||
|
||||
|
|
@ -283,7 +310,6 @@ public class TaxaProcedure extends StandardLocalExternalAlgorithm {
|
|||
for (int i = 0; i < plugin.size(); i++) {
|
||||
|
||||
PluginDescription pluginDescription = plugin.get(i);
|
||||
|
||||
|
||||
AnalysisLogger.getLogger().debug(
|
||||
"For plugin ***" + pluginDescription.getName());
|
||||
|
|
@ -297,9 +323,8 @@ public class TaxaProcedure extends StandardLocalExternalAlgorithm {
|
|||
.entrySet()) {
|
||||
|
||||
Capabilities capability = pluginCapability.getKey();
|
||||
String capabilityName=capability.name().toString();
|
||||
AnalysisLogger.getLogger().debug(
|
||||
capabilityName);
|
||||
String capabilityName = capability.name().toString();
|
||||
AnalysisLogger.getLogger().debug(capabilityName);
|
||||
if (capabilityName.equals("Unfold")) {
|
||||
|
||||
dpU.addEnum(UnfoldDPEnumType.class, pluginDescription
|
||||
|
|
@ -355,13 +380,13 @@ public class TaxaProcedure extends StandardLocalExternalAlgorithm {
|
|||
|
||||
addEnumerateInput(DataProvidersType.values(), dataProvider,
|
||||
"Choose Data Providere", "ALL");
|
||||
AnalysisLogger.getLogger().debug("Dopo DataProvidersType");
|
||||
AnalysisLogger.getLogger().debug("After DataProvidersType");
|
||||
addEnumerateInput(ExtentionDPType.values(), dataProviderExtention,
|
||||
"Choose Expand Option Data Providere", "ALL");
|
||||
AnalysisLogger.getLogger().debug("Dopo ExtentionDPType");
|
||||
AnalysisLogger.getLogger().debug("After ExtentionDPType");
|
||||
addEnumerateInput(UnfoldDPEnumType.values(), dataProviderUnfold,
|
||||
"Choose Unfold Option Data Providere", "ALL");
|
||||
AnalysisLogger.getLogger().debug("Dopo UnfoldDPEnumType");
|
||||
AnalysisLogger.getLogger().debug("After UnfoldDPEnumType");
|
||||
|
||||
inputs.add(tinput);
|
||||
inputs.add(columns);
|
||||
|
|
|
|||
|
|
@ -2,6 +2,11 @@ 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.text.SimpleDateFormat;
|
||||
import java.util.ArrayList;
|
||||
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
|
|
@ -9,147 +14,220 @@ 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;
|
||||
BufferedWriter out;
|
||||
|
||||
private String dataProvider;
|
||||
private String dataProviderUnfold;
|
||||
private String dataProviderExpand;
|
||||
String scope;
|
||||
|
||||
private File tempFile;
|
||||
|
||||
public ThreadExtractionOccFromSPD(ArrayList<String> chunk, String dataProvider,String dataProviderExpand,String dataProviderUnfold,String scope ) {
|
||||
public ThreadExtractionOccFromSPD(ArrayList<String> chunk,
|
||||
String dataProvider, String dataProviderExpand,
|
||||
String dataProviderUnfold, String scope) {
|
||||
this.chunk = chunk;
|
||||
for (String species : chunk) {
|
||||
|
||||
// AnalysisLogger.getLogger().debug(species);
|
||||
}
|
||||
this.dataProvider=dataProvider;
|
||||
this.dataProviderExpand= dataProviderExpand;
|
||||
this.dataProviderUnfold=dataProviderUnfold;
|
||||
informations = new ArrayList<ArrayList<String>>();
|
||||
errors= new ArrayList<String>();
|
||||
this.scope=scope;
|
||||
|
||||
|
||||
this.dataProvider = dataProvider;
|
||||
this.dataProviderExpand = dataProviderExpand;
|
||||
this.dataProviderUnfold = dataProviderUnfold;
|
||||
errors = new ArrayList<String>();
|
||||
this.scope = scope;
|
||||
|
||||
}
|
||||
|
||||
|
||||
public void run() {
|
||||
AnalysisLogger.getLogger().debug("SCOPE *******: "+scope);
|
||||
AnalysisLogger.getLogger().debug("SCOPE " + scope);
|
||||
try {
|
||||
tempFile = File.createTempFile("chunk"
|
||||
+ Thread.currentThread().getId(), ".csv");
|
||||
out = new BufferedWriter(new FileWriter(tempFile, false));
|
||||
} catch (Exception e) {
|
||||
AnalysisLogger.getLogger().error(
|
||||
"Error in the chunk file creation: " + e);
|
||||
}
|
||||
ScopeProvider.instance.set(scope);
|
||||
Manager manager=null;
|
||||
try{
|
||||
Manager manager = null;
|
||||
try {
|
||||
manager = manager().build();
|
||||
|
||||
for (String species : chunk) {
|
||||
if (species != null) {
|
||||
String query = new String();
|
||||
for (String species : chunk) {
|
||||
if (species != null) {
|
||||
String query = new String();
|
||||
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();
|
||||
ArrayList<String> array = crateRowTable(ti);
|
||||
|
||||
|
||||
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));
|
||||
insertInTheFile(array);
|
||||
array = null;
|
||||
System.gc();
|
||||
|
||||
}
|
||||
if (i == 0) {
|
||||
errors.add(species + " not found.");
|
||||
}
|
||||
} catch (Exception e) {
|
||||
errors.add("Exception on " + species + " :"
|
||||
+ e.getMessage());
|
||||
e.printStackTrace();
|
||||
}
|
||||
if(i==0)
|
||||
{
|
||||
errors.add(species+" not found.");
|
||||
}
|
||||
} catch (Exception e) {
|
||||
errors.add("Exception on "+species+" :"+ e.getMessage());
|
||||
e.printStackTrace();
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
}catch(Throwable e){
|
||||
out.close();
|
||||
} catch (Throwable e) {
|
||||
e.printStackTrace();
|
||||
AnalysisLogger.getLogger().debug("An error occurred: "+e.getMessage());
|
||||
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;
|
||||
AnalysisLogger.getLogger().debug("expand is : "+dataProviderExpand);
|
||||
if(dataProviderExpand.equals("ALL"))
|
||||
{expand=" EXPAND";}
|
||||
else{
|
||||
|
||||
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;
|
||||
AnalysisLogger.getLogger().debug("expand is : " + dataProviderExpand);
|
||||
if (dataProviderExpand.equals("ALL")) {
|
||||
expand = " EXPAND";
|
||||
} else {
|
||||
AnalysisLogger.getLogger().debug("inside else ");
|
||||
if(dataProviderExpand.equals("NO OPTION"))
|
||||
expand="";
|
||||
if (dataProviderExpand.equals("NO OPTION"))
|
||||
expand = "";
|
||||
else
|
||||
expand=" EXPAND WITH "+dataProviderExpand;
|
||||
expand = " EXPAND WITH " + dataProviderExpand;
|
||||
}
|
||||
query= query+ expand;
|
||||
query=query+ where;
|
||||
query= query +" RETURN occurrence";
|
||||
query = query + expand;
|
||||
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())));
|
||||
private ArrayList<String> crateRowTable(OccurrencePoint occurrence) {
|
||||
ArrayList<String> infoOcc = new ArrayList<String>();
|
||||
infoOcc.add(occurrence.getInstitutionCode().replace(",", " "));
|
||||
infoOcc.add(occurrence.getCollectionCode().replace(",", " "));
|
||||
infoOcc.add(occurrence.getCatalogueNumber().replace(",", " "));
|
||||
infoOcc.add(occurrence.getDataSet().getName());
|
||||
infoOcc.add(occurrence.getDataSet().getDataProvider().getName());
|
||||
infoOcc.add(occurrence.getProvider());
|
||||
|
||||
infoOcc.add(occurrence.getScientificNameAuthorship());
|
||||
infoOcc.add(occurrence.getIdentifiedBy());
|
||||
|
||||
infoOcc.add(occurrence.getCredits());
|
||||
infoOcc.add(occurrence.getRecordedBy());
|
||||
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd hh:mm:ss");
|
||||
if (occurrence.getEventDate() == null
|
||||
|| sdf.format(occurrence.getEventDate().getTime()).length() == 0)
|
||||
infoOcc.add("");
|
||||
else
|
||||
infoOcc.add(sdf.format(occurrence.getEventDate().getTime()));
|
||||
|
||||
if (occurrence.getModified() == null
|
||||
|| sdf.format(occurrence.getModified().getTime()).length() == 0)
|
||||
infoOcc.add("");
|
||||
else
|
||||
infoOcc.add(sdf.format(occurrence.getModified().getTime()));
|
||||
|
||||
infoOcc.add(occurrence.getScientificName());
|
||||
|
||||
infoOcc.add(occurrence.getKingdom());
|
||||
infoOcc.add(occurrence.getFamily());
|
||||
infoOcc.add(occurrence.getLocality());
|
||||
infoOcc.add(occurrence.getCountry());
|
||||
|
||||
infoOcc.add(occurrence.getCitation());
|
||||
|
||||
infoOcc.add(Double.toString(occurrence.getDecimalLatitude()));
|
||||
|
||||
infoOcc.add(Double.toString(occurrence.getDecimalLongitude()));
|
||||
infoOcc.add(occurrence.getCoordinateUncertaintyInMeters());
|
||||
infoOcc.add(Double.toString(occurrence.getMaxDepth()));
|
||||
|
||||
infoOcc.add(Double.toString(occurrence.getMinDepth()));
|
||||
infoOcc.add(occurrence.getBasisOfRecord().toString());
|
||||
|
||||
return infoOcc;
|
||||
|
||||
|
||||
}
|
||||
public ArrayList<ArrayList<String>> getInfo()
|
||||
{
|
||||
return informations;
|
||||
|
||||
private void insertInTheFile(ArrayList<String> array) throws Exception {
|
||||
// AnalysisLogger.getLogger().debug("INSIDE insertInTheFile");
|
||||
|
||||
// String query = "insert into " + outputtable + st + " values (";
|
||||
String writeString = new String();
|
||||
int i = 0;
|
||||
|
||||
for (String s : array) {
|
||||
if (i == array.size() - 1) {
|
||||
if (s == null)
|
||||
writeString = writeString + " ";
|
||||
else {
|
||||
|
||||
writeString = writeString + s.replace(",", " ");
|
||||
}
|
||||
} else if (s == null)
|
||||
{
|
||||
writeString = writeString + " ,";
|
||||
//index of timestamp value, is needed void field
|
||||
if(i==10||i==11)
|
||||
writeString = writeString + ",";
|
||||
|
||||
}
|
||||
else {
|
||||
|
||||
writeString = writeString + s.replace(",", " ") + ",";
|
||||
}
|
||||
|
||||
i++;
|
||||
|
||||
}
|
||||
// AnalysisLogger.getLogger().debug("record is "+writeString);
|
||||
write(writeString);
|
||||
out.newLine();
|
||||
|
||||
}
|
||||
public ArrayList<String> getErrors()
|
||||
{
|
||||
|
||||
private void write(String writeSt) {
|
||||
try {
|
||||
out.write(writeSt);
|
||||
|
||||
} catch (IOException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public File getInfo() {
|
||||
return tempFile;
|
||||
}
|
||||
|
||||
public ArrayList<String> getErrors() {
|
||||
return errors;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -143,7 +143,7 @@ public class ThreadExtractionTaxaFromSPD implements Runnable {
|
|||
{
|
||||
ArrayList<String> infoOcc= new ArrayList<String>();
|
||||
infoOcc.add(p.getScientificName());
|
||||
infoOcc.add(p.getAuthor());
|
||||
infoOcc.add(p.getScientificNameAuthorship());
|
||||
infoOcc.add(p.getCitation());
|
||||
infoOcc.add(p.getCredits());
|
||||
infoOcc.add(p.getId());
|
||||
|
|
|
|||
|
|
@ -37,9 +37,9 @@ public class AbsoluteSpeciesBarChartsAlgorithm extends
|
|||
static String urlParameterName = "DatabaseURL";
|
||||
protected String fileName;
|
||||
BufferedWriter out;
|
||||
private String firstSpeciesNumber = " SpeciesNumber :";
|
||||
private String yearStart = "Start year :";
|
||||
private String yearEnd = "End year :";
|
||||
private String firstSpeciesNumber = "Species_number";
|
||||
private String yearStart = "Start_year";
|
||||
private String yearEnd = "End_year";
|
||||
private int speciesNumber;
|
||||
String databaseJdbc;
|
||||
String year_start;
|
||||
|
|
@ -56,7 +56,7 @@ public class AbsoluteSpeciesBarChartsAlgorithm extends
|
|||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return ": A transducer algorithm that produces the list of top n most observed taxa, i.e. the species taxa having the largest number of occurrence records, in the OBIS database in a given time interval";
|
||||
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() {
|
||||
|
|
@ -122,7 +122,7 @@ public class AbsoluteSpeciesBarChartsAlgorithm extends
|
|||
"10");
|
||||
addStringInput(yearStart, "Starting year of the analysis", "1800");
|
||||
addStringInput(yearEnd, "Ending year of the analysis", "2020");
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
addRemoteDatabaseInput("TrendyLyzerObis", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -90,7 +90,7 @@ public class SimpleAlgorithm extends StandardLocalExternalAlgorithm{
|
|||
@Override
|
||||
protected void setInputParameters() {
|
||||
addStringInput(species, "Slected species", "Solea solea");
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
addRemoteDatabaseInput("TrendyLyzerObis", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -31,10 +31,10 @@ public class SpeciesObservationsAreaBarChart extends
|
|||
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 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>();
|
||||
|
|
@ -58,9 +58,9 @@ public class SpeciesObservationsAreaBarChart extends
|
|||
"SpeciesObservationsAreaBarChart Initialization");
|
||||
}
|
||||
|
||||
@Override
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "A transducer algorithm that produces a chart reporting single species distribution per area (e.g. LME or MEOW) in the OBIS database in a given time interval for selected species.";
|
||||
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)";
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -135,7 +135,7 @@ public class SpeciesObservationsAreaBarChart extends
|
|||
AreaEnum.LME.name());
|
||||
addStringInput(yearStart, "Starting year of the analysis", "1800");
|
||||
addStringInput(yearEnd, " Ending year of the analysis", "2020");
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
addRemoteDatabaseInput("TrendyLyzerObis", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -40,11 +40,11 @@ public class SpeciesObservationsPerLMEAreaPerYearLineChart extends StandardLocal
|
|||
static String userParameterName = "DatabaseUserName";
|
||||
static String passwordParameterName = "DatabasePassword";
|
||||
static String urlParameterName = "DatabaseURL";
|
||||
private String yearStart = "Start Year";
|
||||
private String yearEnd = "End Year";
|
||||
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 static String area = "Area_type";
|
||||
private String choseArea = "Area_name";
|
||||
private String selectedAreaName;
|
||||
static int justcall=0;
|
||||
private String[] speciesNames;
|
||||
|
|
@ -62,10 +62,10 @@ public class SpeciesObservationsPerLMEAreaPerYearLineChart extends StandardLocal
|
|||
String databaseUser=new String() ;
|
||||
String databasePwd =new String();
|
||||
|
||||
@Override
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
addRemoteDatabaseInput("TrendyLyzerObis", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
if(justcall==0)
|
||||
{ justcall=1;
|
||||
|
|
@ -77,6 +77,7 @@ public class SpeciesObservationsPerLMEAreaPerYearLineChart extends StandardLocal
|
|||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
addEnumerateInput(LMEenumType.values(), area, "Choose the area name",
|
||||
Util.formatAreaName("NORTH SEA"));
|
||||
|
|
@ -175,7 +176,7 @@ public class SpeciesObservationsPerLMEAreaPerYearLineChart extends StandardLocal
|
|||
}
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "A transducer algorithm that calculates the number of species observation in the OBIS database during a given time interval for selected species and LME area.";
|
||||
return "Algorithm returning most observed species in a specific years range (data collected from OBIS database).";
|
||||
|
||||
}
|
||||
public void fulfilParameters() throws IOException {
|
||||
|
|
|
|||
|
|
@ -38,11 +38,11 @@ public class SpeciesObservationsPerMEOWAreaPerYearLineChart extends StandardLoca
|
|||
static String userParameterName = "DatabaseUserName";
|
||||
static String passwordParameterName = "DatabasePassword";
|
||||
static String urlParameterName = "DatabaseURL";
|
||||
private String yearStart = "Start Year";
|
||||
private String yearEnd = "End Year";
|
||||
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 static String area = "Area_type";
|
||||
private String choseArea = "Area_name";
|
||||
private String selectedAreaName;
|
||||
static int justcall=0;
|
||||
private String[] speciesNames;
|
||||
|
|
@ -62,11 +62,10 @@ public class SpeciesObservationsPerMEOWAreaPerYearLineChart extends StandardLoca
|
|||
@Override
|
||||
protected void setInputParameters() {
|
||||
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
addRemoteDatabaseInput("TrendyLyzerObis", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
if(justcall==0)
|
||||
{ justcall=1;
|
||||
|
||||
try {
|
||||
queryArea(getStaticConnection());
|
||||
} catch (Exception e) {
|
||||
|
|
@ -174,7 +173,7 @@ public class SpeciesObservationsPerMEOWAreaPerYearLineChart extends StandardLoca
|
|||
}
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "A transducer algorithm that calculates the number of species observation in the OBIS database during a given time interval for selected species and MEOW area.";
|
||||
return "Algorithm returning most observed species in a specific years range (data collected from OBIS database).";
|
||||
|
||||
}
|
||||
public void fulfilParameters() throws Exception {
|
||||
|
|
|
|||
|
|
@ -37,8 +37,8 @@ public class SpeciesObservationsPerYear extends StandardLocalExternalAlgorithm {
|
|||
static String userParameterName = "DatabaseUserName";
|
||||
static String passwordParameterName = "DatabasePassword";
|
||||
static String urlParameterName = "DatabaseURL";
|
||||
private String yearStart = "Start Year :";
|
||||
private String yearEnd = "End Year :";
|
||||
private String yearStart = "Start_year";
|
||||
private String yearEnd = "End_year";
|
||||
private String[] speciesNames;
|
||||
private TimeSeriesCollection dataset;
|
||||
protected String fileName;
|
||||
|
|
@ -53,7 +53,7 @@ public class SpeciesObservationsPerYear extends StandardLocalExternalAlgorithm {
|
|||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "A transducer algorithm that calculates the number of species observation in the OBIS database per year in a given time interval for selected species.";
|
||||
return "An algorithm producing the trend of the observations for a certain species in a certain years range.";
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -157,7 +157,7 @@ public class SpeciesObservationsPerYear extends StandardLocalExternalAlgorithm {
|
|||
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,
|
||||
addRemoteDatabaseInput("TrendyLyzerObis", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -29,13 +29,13 @@ public class TaxaObservationsBarChartAlgorithm extends StandardLocalExternalAlg
|
|||
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 yearStart = "Start_year";
|
||||
private String yearEnd = "End_year";
|
||||
private String taxa = "Level";
|
||||
String tax;
|
||||
protected String fileName;
|
||||
BufferedWriter out;
|
||||
private String firstTaxaNumber = "TaxaNumber :";
|
||||
private String firstTaxaNumber = "Taxa_number";
|
||||
private int taxaNumber;
|
||||
LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
|
||||
private DefaultCategoryDataset dataset;
|
||||
|
|
@ -48,7 +48,7 @@ public class TaxaObservationsBarChartAlgorithm extends StandardLocalExternalAlg
|
|||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "A transducer algorithm that calculates the number of observations in the OBIS database per year in a given time interval for a selected taxonomic group at a given rank.";
|
||||
return "An algorithm producing a bar chart for the most observed taxa in a certain years range (with respect to the OBIS database)";
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -125,7 +125,7 @@ public class TaxaObservationsBarChartAlgorithm extends StandardLocalExternalAlg
|
|||
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,
|
||||
addRemoteDatabaseInput("TrendyLyzerObis", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -34,9 +34,9 @@ public class TaxaObservationsPerYearLineChart
|
|||
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 yearStart = "Start_year";
|
||||
private String yearEnd = "End_year";
|
||||
private String taxa = "Level";
|
||||
private String tax;
|
||||
|
||||
private String[] taxaNames;
|
||||
|
|
@ -145,7 +145,7 @@ public class TaxaObservationsPerYearLineChart
|
|||
super.inputs.add(taxaSelected);
|
||||
|
||||
// addStringInput("Species", "The species", config.getParam("Species"));
|
||||
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
|
||||
addRemoteDatabaseInput("TrendyLyzerObis", urlParameterName,
|
||||
userParameterName, passwordParameterName, "driver", "dialect");
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue