git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineExternalAlgorithms@124652 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
parent
f27b50e127
commit
874c3e203a
2
.project
2
.project
|
|
@ -1,6 +1,6 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<projectDescription>
|
||||
<name>ecological-engine-external-algorithms</name>
|
||||
<name>ecological-engine-external-algorithms1.1.5</name>
|
||||
<comment></comment>
|
||||
<projects>
|
||||
</projects>
|
||||
|
|
|
|||
|
|
@ -1,2 +1,6 @@
|
|||
v. 1.0.0 (19-03-2013)
|
||||
* First release
|
||||
v. 1.1.5 (05-09-2014)
|
||||
* Geothermal analysis
|
||||
v. 1.1.6 (30-06-2015)
|
||||
* Introducing average annual precipitation
|
||||
v. 1.1.7 (23-09-2015)
|
||||
* Adding algorithms by univ Brazil
|
||||
|
|
@ -17,7 +17,7 @@ Authors
|
|||
Version and Release Date
|
||||
------------------------
|
||||
|
||||
version 1.0.0 (19-04-2013)
|
||||
version 1.1.7 (23-09-2015)
|
||||
|
||||
Description
|
||||
--------------------
|
||||
|
|
@ -29,7 +29,7 @@ Download information
|
|||
--------------------
|
||||
|
||||
Source code is available from SVN:
|
||||
http://svn.research-infrastructures.eu/d4science/gcube/trunk/content-management/EcologicalModelling
|
||||
https://svn.d4science.research-infrastructures.eu/gcube/branches/data-analysis/EcologicalEngineExternalAlgorithms/1.1/
|
||||
|
||||
Binaries can be downloaded from:
|
||||
http://software.d4science.research-infrastructures.eu/
|
||||
|
|
|
|||
|
|
@ -10,4 +10,13 @@
|
|||
<Changeset component="${build.finalName}" date="2013-10-22">
|
||||
<Change>Fix problem in species/taxa procedures </Change>
|
||||
</Changeset>
|
||||
<Changeset component="${build.finalName}" date="2014-09-05">
|
||||
<Change>Geothermal analysis </Change>
|
||||
</Changeset>
|
||||
<Changeset component="${build.finalName}" date="2015-06-30">
|
||||
<Change>Introducing average annual precipitation</Change>
|
||||
</Changeset>
|
||||
<Changeset component="${build.finalName}" date="2015-09-23">
|
||||
<Change>Adding algorithms by univ Brazil</Change>
|
||||
</Changeset>
|
||||
</ReleaseNotes>
|
||||
|
|
@ -1 +1 @@
|
|||
https://svn.d4science.research-infrastructures.eu/gcube/branches/data-analysis/EcologicalEngineExternalAlgorithms/1.0
|
||||
https://svn.d4science.research-infrastructures.eu/gcube/branches/data-analysis/EcologicalEngineExternalAlgorithms/1.1/
|
||||
85
pom.xml
85
pom.xml
|
|
@ -9,7 +9,7 @@
|
|||
</parent>
|
||||
<groupId>org.gcube.dataanalysis</groupId>
|
||||
<artifactId>ecological-engine-external-algorithms</artifactId>
|
||||
<version>1.1.7-SNAPSHOT</version>
|
||||
<version>1.1.8-SNAPSHOT</version>
|
||||
<name>ecological-engine-external-algorithms</name>
|
||||
<description>ecological-engine-external-algorithms library</description>
|
||||
<properties>
|
||||
|
|
@ -26,54 +26,15 @@
|
|||
<artifactId>taxamatchpostgres</artifactId>
|
||||
<version>1.2.0</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>postgresql</groupId>
|
||||
<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>
|
||||
<version>[1.0.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.core</groupId>
|
||||
<artifactId>common-encryption</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>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.slf4j</groupId>
|
||||
<artifactId>slf4j-api</artifactId>
|
||||
<version>1.6.4</version>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>log4j</groupId>
|
||||
<artifactId>log4j</artifactId>
|
||||
<version>1.2.16</version>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.slf4j</groupId>
|
||||
<artifactId>slf4j-log4j12</artifactId>
|
||||
<version>1.6.4</version>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.gcube.data.spd</groupId>
|
||||
<artifactId>spd-client-library</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT, 4.0.0-SNAPSHOT)</version>
|
||||
<version>[1.0.0, 4.0.0)</version>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>org.gcube.data.spd</groupId>
|
||||
|
|
@ -81,8 +42,6 @@
|
|||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
<!-- This dependency is needed and is need on TOP to use GWT UI BInder
|
||||
without old Xerces version of gCore complaining -->
|
||||
<dependency>
|
||||
<groupId>xerces</groupId>
|
||||
<artifactId>xercesImpl</artifactId>
|
||||
|
|
@ -92,54 +51,20 @@
|
|||
<dependency>
|
||||
<groupId>org.gcube.data.spd</groupId>
|
||||
<artifactId>spql-parser</artifactId>
|
||||
<version>[2.0.0-SNAPSHOT, 3.0.0-SNAPSHOT)</version>
|
||||
<version>[2.0.0, 3.0.0)</version>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.common</groupId>
|
||||
<artifactId>csv4j</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
|
||||
<version>[1.0.0, 2.0.0)</version>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.data.spd</groupId>
|
||||
<artifactId>spd-model</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT, 4.0.0-SNAPSHOT)</version>
|
||||
<version>[1.0.0, 4.0.0)</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>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<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>
|
||||
</dependency>
|
||||
|
||||
|
||||
|
||||
<dependency>
|
||||
<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>
|
||||
</dependency>
|
||||
|
||||
</dependencies>
|
||||
<repositories>
|
||||
<repository>
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@ package org.gcube.dataanalysis.fin.taxamatch;
|
|||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import org.apache.bcel.generic.ALOAD;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.ColumnTypesList;
|
||||
|
|
|
|||
|
|
@ -1,192 +0,0 @@
|
|||
package org.gcube.dataanalysis.precipitations;
|
||||
|
||||
import java.text.ParseException;
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Calendar;
|
||||
import java.util.Date;
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
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.ServiceType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
||||
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.hibernate.SessionFactory;
|
||||
|
||||
public class AnnualPrecipitation extends StandardLocalExternalAlgorithm {
|
||||
// Class Attributes
|
||||
String outputtablename;
|
||||
String outputtable;
|
||||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "This is a simple algorithm that returns the annual precipitation. The input is a general tabular resource with two columns (date and precipitation).";
|
||||
}
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
AnalysisLogger.getLogger().debug("Initialization");
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void process() throws Exception {
|
||||
// Recovering data
|
||||
config.setParam("DatabaseDriver", "org.postgresql.Driver");
|
||||
SessionFactory dbconnection = DatabaseUtils.initDBSession(config);
|
||||
try {
|
||||
String tablename = getInputParameter("PrecTable");
|
||||
String columnnames = getInputParameter("PrecColumns");
|
||||
outputtablename = getInputParameter("OutputTableName");
|
||||
outputtable = getInputParameter("OutputTable");
|
||||
String[] columnlist = columnnames.split(AlgorithmConfiguration.getListSeparator());
|
||||
List<Object> dataList = DatabaseFactory.executeSQLQuery("select " + columnlist[0] + " from " + tablename + " order by " + columnlist[0] + " asc", dbconnection);
|
||||
List<Object> precList = DatabaseFactory.executeSQLQuery("select " + columnlist[1] + " from " + tablename + " order by " + columnlist[0] + " asc", dbconnection);
|
||||
// Business Logic
|
||||
AnalysisLogger.getLogger().info("Creating output table [" + "create table " + outputtable + " (year integer, value real)]");
|
||||
DatabaseFactory.executeSQLUpdate("create table " + outputtable + " (year integer, value real)", dbconnection);
|
||||
Double averageValue = new Double(0);
|
||||
for (int i = 0; i < dataList.size(); i++) { // for each line
|
||||
if (i == 0) { // first iteration
|
||||
averageValue = averageValue + Double.parseDouble(String.valueOf(precList.get(i)));
|
||||
if (dataList.size() == 1) { // if first iteration is also
|
||||
// the last
|
||||
Date currentDate = anyStringToDate(String.valueOf(dataList.get(i)));
|
||||
AnalysisLogger.getLogger().info("i=0 Current Date: "+currentDate);
|
||||
Calendar currentDateCal = Calendar.getInstance();
|
||||
currentDateCal.setTime(currentDate);
|
||||
int yearCurrentDate = currentDateCal.get(Calendar.YEAR);
|
||||
AnalysisLogger.getLogger().info("Inserting into table " + "insert into " + outputtable + " (year,value) values (" + yearCurrentDate + "," + averageValue + ")");
|
||||
DatabaseFactory.executeSQLUpdate("insert into " + outputtable + " (year,value) values (" + yearCurrentDate + "," + averageValue + ")", dbconnection);
|
||||
averageValue = new Double(0);
|
||||
}
|
||||
}
|
||||
if (i > 0) { // other iterations
|
||||
Date currentDate = anyStringToDate(String.valueOf(dataList.get(i)));
|
||||
Date lastDate = anyStringToDate(String.valueOf(dataList.get(i - 1)));
|
||||
AnalysisLogger.getLogger().info("Current Date: "+currentDate);
|
||||
AnalysisLogger.getLogger().info("Last Date: "+lastDate);
|
||||
Calendar currentDateCal = Calendar.getInstance();
|
||||
currentDateCal.setTime(currentDate);
|
||||
int yearCurrentDate = currentDateCal.get(Calendar.YEAR);
|
||||
Calendar lastDateCal = Calendar.getInstance();
|
||||
lastDateCal.setTime(lastDate);
|
||||
int yearLastDate = lastDateCal.get(Calendar.YEAR);
|
||||
if (yearCurrentDate > yearLastDate) {
|
||||
// inserting average annual
|
||||
AnalysisLogger.getLogger().info("Inserting into table " + "insert into " + outputtable + " (year,value) values (" + yearLastDate + "," + averageValue + ")");
|
||||
DatabaseFactory.executeSQLUpdate("insert into " + outputtable + " (year,value) values (" + yearLastDate + "," + averageValue + ")", dbconnection);
|
||||
averageValue = new Double(0);
|
||||
averageValue = new Double(String.valueOf(precList.get(i)));
|
||||
} else {
|
||||
averageValue = averageValue + Double.parseDouble(String.valueOf(precList.get(i)));
|
||||
}
|
||||
}
|
||||
if (i != 0 && i == dataList.size() - 1) { // last iteration
|
||||
Date currentDate = anyStringToDate(String.valueOf(dataList.get(i)));
|
||||
Calendar currentDateCal = Calendar.getInstance();
|
||||
currentDateCal.setTime(currentDate);
|
||||
int yearCurrentDate = currentDateCal.get(Calendar.YEAR);
|
||||
AnalysisLogger.getLogger().info("Inserting into table " + "insert into " + outputtable + " (year,value) values (" + yearCurrentDate + "," + averageValue + ")");
|
||||
DatabaseFactory.executeSQLUpdate("insert into " + outputtable + " (year,value) values (" + yearCurrentDate + "," + averageValue + ")", dbconnection);
|
||||
averageValue = new Double(0);
|
||||
}
|
||||
}
|
||||
} catch (Exception e) {
|
||||
AnalysisLogger.getLogger().error(e.getMessage());
|
||||
throw e;
|
||||
} finally {
|
||||
DatabaseUtils.closeDBConnection(dbconnection);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
// First parameter: Internal tabular resource
|
||||
List<TableTemplates> templates = new ArrayList<TableTemplates>();
|
||||
templates.add(TableTemplates.GENERIC);
|
||||
InputTable tinput = new InputTable(templates, "PrecTable", "Precipitation tabular resource");
|
||||
ColumnTypesList columns = new ColumnTypesList("PrecTable", "PrecColumns", "Selected columns for date and precipitation", false);
|
||||
inputs.add(tinput);
|
||||
inputs.add(columns);
|
||||
// Second parameter: Output table
|
||||
ServiceType randomstring = new ServiceType(ServiceParameters.RANDOMSTRING, "OutputTable", "", "prec");
|
||||
inputs.add(randomstring);
|
||||
DatabaseType.addDefaultDBPars(inputs);
|
||||
// Third parameter: Output table name
|
||||
addStringInput("OutputTableName", "The name of the output table", "prec_");
|
||||
}
|
||||
|
||||
@Override
|
||||
public StatisticalType getOutput() {
|
||||
List<TableTemplates> outtemplate = new ArrayList<TableTemplates>();
|
||||
outtemplate.add(TableTemplates.GENERIC);
|
||||
OutputTable out = new OutputTable(outtemplate, outputtablename, outputtable, "The output table containing all the matches");
|
||||
return out;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
AnalysisLogger.getLogger().debug("Shutdown");
|
||||
}
|
||||
|
||||
/**
|
||||
* An auxiliary method that converts string to date
|
||||
*
|
||||
* @param value
|
||||
* @return
|
||||
*/
|
||||
public static Date anyStringToDate(String value) {
|
||||
Date date = null;
|
||||
try {
|
||||
if (isValidFormat("yyyy-mm-dd", value)) {
|
||||
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-mm-dd");
|
||||
date = sdf.parse(value);
|
||||
}
|
||||
if (isValidFormat("yyyymmdd", value)) {
|
||||
SimpleDateFormat sdf = new SimpleDateFormat("yyyymmdd");
|
||||
date = sdf.parse(value);
|
||||
}
|
||||
if (isValidFormat("dd/mm/yyyy", value)) {
|
||||
SimpleDateFormat sdf = new SimpleDateFormat("dd/mm/yyyy");
|
||||
date = sdf.parse(value);
|
||||
}
|
||||
if (isValidFormat("dd-mm-yyyy", value)) {
|
||||
SimpleDateFormat sdf = new SimpleDateFormat("dd-mm-yyyy");
|
||||
date = sdf.parse(value);
|
||||
}
|
||||
} catch (Exception e) {
|
||||
date = null;
|
||||
}
|
||||
return date;
|
||||
}
|
||||
|
||||
/**
|
||||
* An auxiliary method that validates if a string respect a specified date format
|
||||
*
|
||||
* @param format
|
||||
* @param value
|
||||
* @return
|
||||
*/
|
||||
public static boolean isValidFormat(String format, String value) {
|
||||
Date date = null;
|
||||
try {
|
||||
SimpleDateFormat sdf = new SimpleDateFormat(format);
|
||||
date = sdf.parse(value);
|
||||
if (!value.equals(sdf.format(date))) {
|
||||
date = null;
|
||||
}
|
||||
} catch (ParseException ex) {
|
||||
date = null;
|
||||
}
|
||||
return date != null;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,49 +0,0 @@
|
|||
package org.gcube.dataanalysis.test;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.UUID;
|
||||
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory;
|
||||
import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
|
||||
|
||||
public class TestAverageAnnualPrecipitation {
|
||||
|
||||
/**
|
||||
* @param args
|
||||
*/
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
System.out.println("TEST of PREC ALGO 1");
|
||||
List<ComputationalAgent> trans = null;
|
||||
trans = TransducerersFactory.getTransducerers(testConfig());
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
StatisticalType st = trans.get(0).getOutput();
|
||||
trans = null;
|
||||
}
|
||||
|
||||
private static AlgorithmConfiguration testConfig() {
|
||||
AlgorithmConfiguration config = Regressor.getConfig();
|
||||
config.setConfigPath("./cfg/");
|
||||
config.setPersistencePath("./");
|
||||
|
||||
config.setAgent("AVERAGE_ANNUAL_PREC");
|
||||
|
||||
config.setParam("DatabaseUserName","postgres");
|
||||
config.setParam("DatabasePassword","postgres");
|
||||
config.setParam("DatabaseURL","jdbc:postgresql://localhost");
|
||||
config.setParam("DatabaseDriver","org.postgresql.Driver");
|
||||
config.setParam("PrecTable", "test");
|
||||
config.setParam("PrecColumns", "day" + AlgorithmConfiguration.listSeparator + "precipitation");
|
||||
String tablename = "testprec" + (UUID.randomUUID());
|
||||
|
||||
config.setParam("OutputTableName", "Test Prec");
|
||||
config.setParam("OutputTable", tablename.replace("-", ""));
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
package org.gube.examples;
|
||||
package org.gcube.examples;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileWriter;
|
||||
|
|
@ -1,25 +0,0 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<Resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<ID></ID>
|
||||
<Type>Library</Type>
|
||||
<Profile>
|
||||
<Description>Ecological Engine Library</Description>
|
||||
<Class>EcologicalEngineExternalAlgorithms</Class>
|
||||
<Name>ecological-engine-external-algorithms</Name>
|
||||
<Version>1.1.1</Version>
|
||||
<Packages>
|
||||
<Software>
|
||||
<Name>ecological-engine-external-algorithms</Name>
|
||||
<Version>1.1.7-SNAPSHOT</Version>
|
||||
<MavenCoordinates>
|
||||
<groupId>org.gcube.dataanalysis</groupId>
|
||||
<artifactId>ecological-engine-external-algorithms</artifactId>
|
||||
<version>1.1.7-SNAPSHOT</version>
|
||||
</MavenCoordinates>
|
||||
<Files>
|
||||
<File>ecological-engine-external-algorithms-1.1.7-SNAPSHOT.jar</File>
|
||||
</Files>
|
||||
</Software>
|
||||
</Packages>
|
||||
</Profile>
|
||||
</Resource>
|
||||
Loading…
Reference in New Issue