release 4.3
git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/branches/data-access/gbif-spd-plugin/1.9@142049 82a268e6-3cf1-43bd-a215-b396298e98cfmaster
commit
6bab244632
@ -0,0 +1,10 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<classpath>
|
||||
<classpathentry kind="src" output="target/classes" path="src/main/java"/>
|
||||
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
|
||||
<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
|
||||
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources"/>
|
||||
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
|
||||
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
|
||||
<classpathentry kind="output" path="target/classes"/>
|
||||
</classpath>
|
||||
@ -0,0 +1,23 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<projectDescription>
|
||||
<name>gbif-plugin</name>
|
||||
<comment></comment>
|
||||
<projects>
|
||||
</projects>
|
||||
<buildSpec>
|
||||
<buildCommand>
|
||||
<name>org.eclipse.jdt.core.javabuilder</name>
|
||||
<arguments>
|
||||
</arguments>
|
||||
</buildCommand>
|
||||
<buildCommand>
|
||||
<name>org.eclipse.m2e.core.maven2Builder</name>
|
||||
<arguments>
|
||||
</arguments>
|
||||
</buildCommand>
|
||||
</buildSpec>
|
||||
<natures>
|
||||
<nature>org.eclipse.jdt.core.javanature</nature>
|
||||
<nature>org.eclipse.m2e.core.maven2Nature</nature>
|
||||
</natures>
|
||||
</projectDescription>
|
||||
@ -0,0 +1,7 @@
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||||
#Tue Feb 14 11:06:25 CET 2012
|
||||
eclipse.preferences.version=1
|
||||
encoding//src/main/java=UTF-8
|
||||
encoding//src/main/resources=UTF-8
|
||||
encoding//src/test/java=UTF-8
|
||||
encoding//src/test/resources=UTF-8
|
||||
encoding/<project>=UTF-8
|
||||
@ -0,0 +1,6 @@
|
||||
#Tue Feb 14 11:06:25 CET 2012
|
||||
eclipse.preferences.version=1
|
||||
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
|
||||
org.eclipse.jdt.core.compiler.compliance=1.6
|
||||
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
|
||||
org.eclipse.jdt.core.compiler.source=1.6
|
||||
@ -0,0 +1,5 @@
|
||||
#Mon Feb 13 12:19:08 CET 2012
|
||||
activeProfiles=
|
||||
eclipse.preferences.version=1
|
||||
resolveWorkspaceProjects=true
|
||||
version=1
|
||||
@ -0,0 +1 @@
|
||||
${gcube.license}
|
||||
@ -0,0 +1,61 @@
|
||||
The gCube System - ${name}
|
||||
--------------------------------------------------
|
||||
|
||||
${description}
|
||||
|
||||
|
||||
${gcube.description}
|
||||
|
||||
${gcube.funding}
|
||||
|
||||
|
||||
Version
|
||||
--------------------------------------------------
|
||||
|
||||
${version} (${buildDate})
|
||||
|
||||
Please see the file named "changelog.xml" in this directory for the release notes.
|
||||
|
||||
|
||||
Authors
|
||||
--------------------------------------------------
|
||||
|
||||
* Lucio Lelii (lucio.lelii-AT-isti.cnr.it), CNR, Italy
|
||||
|
||||
MAINTAINERS
|
||||
--------------------------------------------------
|
||||
|
||||
* Lucio Lelii (lucio.lelii-AT-isti.cnr.it), CNR, Italy
|
||||
|
||||
Download information
|
||||
--------------------------------------------------
|
||||
|
||||
Source code is available from SVN:
|
||||
${scm.url}
|
||||
|
||||
Binaries can be downloaded from the gCube website:
|
||||
${gcube.website}
|
||||
|
||||
|
||||
Installation
|
||||
--------------------------------------------------
|
||||
|
||||
Installation documentation is available on-line in the gCube Wiki:
|
||||
${gcube.wikiRoot}
|
||||
|
||||
Documentation
|
||||
--------------------------------------------------
|
||||
|
||||
Documentation is available on-line in the gCube Wiki:
|
||||
${gcube.wikiRoot}
|
||||
Support
|
||||
--------------------------------------------------
|
||||
|
||||
Bugs and support requests can be reported in the gCube issue tracking tool:
|
||||
${gcube.issueTracking}
|
||||
|
||||
|
||||
Licensing
|
||||
--------------------------------------------------
|
||||
|
||||
This software is licensed under the terms you may find in the file named "LICENSE" in this directory.
|
||||
@ -0,0 +1,30 @@
|
||||
<ReleaseNotes>
|
||||
<Changeset component="org.gcube.data-access.gbif-spd-plugin.1-0-0" date="2012-05-04">
|
||||
<Change>GBIF plugin for species product discovery first release</Change>
|
||||
</Changeset>
|
||||
<Changeset component="org.gcube.data-access.gbif-spd-plugin.1-1-0" date="2012-09-14">
|
||||
<Change>bug fixing</Change>
|
||||
</Changeset>
|
||||
<Changeset component="org.gcube.data-access.gbif-spd-plugin.1-2-0" date="2012-09-14">
|
||||
<Change>info for repository added</Change>
|
||||
<Change>added more credits on occurrences</Change>
|
||||
</Changeset>
|
||||
<Changeset component="org.gcube.data-access.gbif-spd-plugin.1-3-0" date="2012-09-14">
|
||||
<Change>porting to the spd fwk 1.2.0</Change>
|
||||
</Changeset>
|
||||
<Changeset component="org.gcube.data-access.gbif-spd-plugin.1-4-0" date="2013-01-17">
|
||||
<Change>porting to the spd fwk 2.0.0</Change>
|
||||
</Changeset>
|
||||
<Changeset component="org.gcube.data-access.gbif-spd-plugin.1-6-0" date="2013-05-02">
|
||||
<Change>porting to the spd fwk 2.2.0</Change>
|
||||
</Changeset>
|
||||
<Changeset component="org.gcube.data-access.gbif-spd-plugin.1-7-0" date="2013-07-18">
|
||||
<Change>Sync with spd-model-library changes</Change>
|
||||
</Changeset>
|
||||
<Changeset component="org.gcube.data-access.gbif-spd-plugin.1-8-2" date="2015-06-29">
|
||||
<Change>new matching elements for basis of record added</Change>
|
||||
</Changeset>
|
||||
<Changeset component="org.gcube.data-access.gbif-spd-plugin.1-9-0" date="2017-02-01">
|
||||
<Change>gCore dependencies removed</Change>
|
||||
</Changeset>
|
||||
</ReleaseNotes>
|
||||
@ -0,0 +1,31 @@
|
||||
<assembly
|
||||
xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
|
||||
<id>servicearchive</id>
|
||||
<formats>
|
||||
<format>tar.gz</format>
|
||||
</formats>
|
||||
<baseDirectory>/</baseDirectory>
|
||||
<fileSets>
|
||||
<fileSet>
|
||||
<directory>${distroDirectory}</directory>
|
||||
<outputDirectory>/</outputDirectory>
|
||||
<useDefaultExcludes>true</useDefaultExcludes>
|
||||
<includes>
|
||||
<include>README</include>
|
||||
<include>LICENSE</include>
|
||||
<include>profile.xml</include>
|
||||
<include>changelog.xml</include>
|
||||
</includes>
|
||||
<fileMode>755</fileMode>
|
||||
<filtered>true</filtered>
|
||||
</fileSet>
|
||||
</fileSets>
|
||||
<files>
|
||||
<file>
|
||||
<source>target/${build.finalName}.jar</source>
|
||||
<outputDirectory>/${artifactId}</outputDirectory>
|
||||
</file>
|
||||
</files>
|
||||
</assembly>
|
||||
@ -0,0 +1,28 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<Resource>
|
||||
<ID></ID>
|
||||
<Type>Service</Type>
|
||||
<Profile>
|
||||
<Description>${description}</Description>
|
||||
<Class>DataAccess</Class>
|
||||
<Name>${artifactId}</Name>
|
||||
<Version>1.0.0</Version>
|
||||
<Packages>
|
||||
<Software>
|
||||
<Description>${description}</Description>
|
||||
<Name>${artifactId}</Name>
|
||||
<Version>${version}</Version>
|
||||
<MavenCoordinates>
|
||||
<groupId>${groupId}</groupId>
|
||||
<artifactId>${artifactId}</artifactId>
|
||||
<version>${version}</version>
|
||||
</MavenCoordinates>
|
||||
<Type>library</Type>
|
||||
<Files>
|
||||
<File>${build.finalName}.jar</File>
|
||||
</Files>
|
||||
</Software>
|
||||
</Packages>
|
||||
</Profile>
|
||||
</Resource>
|
||||
|
||||
@ -0,0 +1,149 @@
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<parent>
|
||||
<artifactId>maven-parent</artifactId>
|
||||
<groupId>org.gcube.tools</groupId>
|
||||
<version>1.0.0</version>
|
||||
<relativePath />
|
||||
</parent>
|
||||
|
||||
<groupId>org.gcube.data.spd</groupId>
|
||||
<artifactId>gbif-spd-plugin</artifactId>
|
||||
<version>1.9.0-SNAPSHOT</version>
|
||||
<name>GBIFPlugin</name>
|
||||
<description>gbif plugin for species manager service</description>
|
||||
|
||||
<properties>
|
||||
<distroDirectory>${project.basedir}/distro</distroDirectory>
|
||||
<jackson.version>2.4.4</jackson.version>
|
||||
</properties>
|
||||
|
||||
<dependencyManagement>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>org.gcube.distribution</groupId>
|
||||
<artifactId>gcube-bom</artifactId>
|
||||
<version>LATEST</version>
|
||||
<type>pom</type>
|
||||
<scope>import</scope>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
</dependencyManagement>
|
||||
|
||||
<dependencies>
|
||||
|
||||
<!-- lombok -->
|
||||
<dependency>
|
||||
<groupId>org.projectlombok</groupId>
|
||||
<artifactId>lombok</artifactId>
|
||||
<version>1.16.2</version>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>com.fasterxml.jackson.core</groupId>
|
||||
<artifactId>jackson-databind</artifactId>
|
||||
<version>${jackson.version}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.fasterxml.jackson.core</groupId>
|
||||
<artifactId>jackson-annotations</artifactId>
|
||||
<version>${jackson.version}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.fasterxml.jackson.core</groupId>
|
||||
<artifactId>jackson-core</artifactId>
|
||||
<version>${jackson.version}</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>com.sun.jersey</groupId>
|
||||
<artifactId>jersey-client</artifactId>
|
||||
<version>1.19</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.data.spd</groupId>
|
||||
<artifactId>spd-plugin-framework</artifactId>
|
||||
<version>[3.0.0-SNAPSHOT, 4.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
|
||||
|
||||
<dependency>
|
||||
<groupId>junit</groupId>
|
||||
<artifactId>junit</artifactId>
|
||||
<version>4.11</version>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>ch.qos.logback</groupId>
|
||||
<artifactId>logback-classic</artifactId>
|
||||
<version>1.0.13</version>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
</dependencies>
|
||||
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-compiler-plugin</artifactId>
|
||||
<version>3.1</version>
|
||||
<configuration>
|
||||
<compilerVersion>1.7</compilerVersion>
|
||||
<source>1.7</source>
|
||||
<target>1.7</target>
|
||||
</configuration>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-resources-plugin</artifactId>
|
||||
<version>2.5</version>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>copy-profile</id>
|
||||
<phase>install</phase>
|
||||
<goals>
|
||||
<goal>copy-resources</goal>
|
||||
</goals>
|
||||
<configuration>
|
||||
<outputDirectory>target</outputDirectory>
|
||||
<resources>
|
||||
<resource>
|
||||
<directory>${distroDirectory}</directory>
|
||||
<filtering>true</filtering>
|
||||
<includes>
|
||||
<include>profile.xml</include>
|
||||
</includes>
|
||||
</resource>
|
||||
</resources>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
<version>2.2</version>
|
||||
<configuration>
|
||||
<descriptors>
|
||||
<descriptor>${distroDirectory}/descriptor.xml</descriptor>
|
||||
</descriptors>
|
||||
</configuration>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>servicearchive</id>
|
||||
<phase>install</phase>
|
||||
<goals>
|
||||
<goal>single</goal>
|
||||
</goals>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</project>
|
||||
@ -0,0 +1,22 @@
|
||||
package org.gcube.data.spd.gbifplugin;
|
||||
|
||||
import javax.xml.namespace.QName;
|
||||
|
||||
public class Constants {
|
||||
|
||||
//public static final String BASE_URL = "http://api.gbif.org/v1";
|
||||
|
||||
public static final int QUERY_LIMIT = 200;
|
||||
|
||||
public static final QName GBIFKEY_ATTR= new QName("gbifKey");
|
||||
public static final QName ABOUT_ATTR= new QName("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "about");
|
||||
public static final QName RESOURCE_ATTR= new QName("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "resource");
|
||||
public static final QName TOTAL_MATCHED_ATTR = new QName("totalMatched");
|
||||
|
||||
|
||||
|
||||
public static final String CHILD_RELATIONSHIP_VALUE = "http://rs.tdwg.org/ontology/voc/TaxonConcept#IsChildTaxonOf";
|
||||
|
||||
public static final String REPOSITORY_NAME="GBIF";
|
||||
|
||||
}
|
||||
@ -0,0 +1,84 @@
|
||||
package org.gcube.data.spd.gbifplugin;
|
||||
|
||||
import java.util.Collections;
|
||||
import java.util.Set;
|
||||
|
||||
import org.gcube.common.resources.gcore.ServiceEndpoint;
|
||||
import org.gcube.data.spd.gbifplugin.capabilities.OccurrencesCapabilityImpl;
|
||||
import org.gcube.data.spd.gbifplugin.search.ResultItemSearch;
|
||||
import org.gcube.data.spd.model.Condition;
|
||||
import org.gcube.data.spd.model.RepositoryInfo;
|
||||
import org.gcube.data.spd.model.exceptions.StreamBlockingException;
|
||||
import org.gcube.data.spd.model.products.ResultItem;
|
||||
import org.gcube.data.spd.model.util.Capabilities;
|
||||
import org.gcube.data.spd.plugin.fwk.AbstractPlugin;
|
||||
import org.gcube.data.spd.plugin.fwk.capabilities.OccurrencesCapability;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ObjectWriter;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
|
||||
public class GBIFPlugin extends AbstractPlugin{
|
||||
|
||||
private static Logger logger = LoggerFactory.getLogger(GBIFPlugin.class);
|
||||
|
||||
|
||||
private OccurrencesCapability occurrencesCapability;
|
||||
private String baseURL;
|
||||
|
||||
|
||||
@Override
|
||||
public void initialize(ServiceEndpoint resource) throws Exception {
|
||||
baseURL = resource.profile().accessPoints().iterator().next().address();
|
||||
occurrencesCapability = new OccurrencesCapabilityImpl(baseURL);
|
||||
setUseCache(true);
|
||||
super.initialize(resource);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Set<Capabilities> getSupportedCapabilities() {
|
||||
return Collections.singleton(Capabilities.Occurrence);
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
public OccurrencesCapability getOccurrencesInterface() {
|
||||
return occurrencesCapability;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getRepositoryName() {
|
||||
return "GBIF";
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getDescription() {
|
||||
return "A plugin for GBIF interaction";
|
||||
}
|
||||
|
||||
@Override
|
||||
public void searchByScientificName(String word, ObjectWriter<ResultItem> writer,
|
||||
Condition... properties) {
|
||||
logger.debug("starting the search for gbifPlugin with word "+word);
|
||||
try {
|
||||
new ResultItemSearch(baseURL, word, properties).search(writer,Constants.QUERY_LIMIT);
|
||||
} catch (Exception e) {
|
||||
logger.debug("searchByScientificName failed",e);
|
||||
writer.write(new StreamBlockingException(Constants.REPOSITORY_NAME, word));
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public RepositoryInfo getRepositoryInfo() {
|
||||
return new RepositoryInfo(
|
||||
"http://www.gbif.org/fileadmin/templates/main/images/logo_leaf.gif",
|
||||
"http://www.gbif.org/",
|
||||
"The Global Biodiversity Information Facility (GBIF) was established by governments in 2001 to encourage free and open access to biodiversity data, " +
|
||||
"via the Internet. Through a global network of countries and organizations, GBIF promotes and facilitates the mobilization, access, " +
|
||||
"discovery and use of information about the occurrence of organisms over time and across the planet");
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,110 @@
|
||||
package org.gcube.data.spd.gbifplugin.capabilities;
|
||||
|
||||
import java.util.HashSet;
|
||||
import java.util.Iterator;
|
||||
import java.util.Set;
|
||||
|
||||
import org.gcube.data.spd.gbifplugin.Constants;
|
||||
import org.gcube.data.spd.gbifplugin.search.OccurrenceSearch;
|
||||
import org.gcube.data.spd.model.Condition;
|
||||
import org.gcube.data.spd.model.Conditions;
|
||||
import org.gcube.data.spd.model.exceptions.StreamBlockingException;
|
||||
import org.gcube.data.spd.model.exceptions.StreamNonBlockingException;
|
||||
import org.gcube.data.spd.model.products.OccurrencePoint;
|
||||
import org.gcube.data.spd.plugin.fwk.capabilities.OccurrencesCapability;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ClosableWriter;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ObjectWriter;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public class OccurrencesCapabilityImpl extends OccurrencesCapability{
|
||||
|
||||
|
||||
private static Logger logger = LoggerFactory.getLogger(OccurrencesCapabilityImpl.class);
|
||||
|
||||
private String baseUrl;
|
||||
|
||||
|
||||
|
||||
public OccurrencesCapabilityImpl(String baseUrl) {
|
||||
super();
|
||||
this.baseUrl = baseUrl;
|
||||
}
|
||||
|
||||
|
||||
|
||||
@SuppressWarnings("serial")
|
||||
@Override
|
||||
public Set<Conditions> getSupportedProperties() {
|
||||
return new HashSet<Conditions>(){{
|
||||
add(Conditions.DATE);
|
||||
add(Conditions.COORDINATE);
|
||||
|
||||
}};
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
public void searchByScientificName(String word,
|
||||
ObjectWriter<OccurrencePoint> writer, Condition... properties) {
|
||||
try{
|
||||
new OccurrenceSearch(baseUrl).search(writer, word, Constants.QUERY_LIMIT, properties);
|
||||
} catch (Exception e) {
|
||||
logger.debug("search occurrences by ScientificName failed",e);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void getOccurrencesByProductKeys(
|
||||
ClosableWriter<OccurrencePoint> writer, Iterator<String> keys) {
|
||||
OccurrenceSearch occSearch = null;
|
||||
try{
|
||||
occSearch = new OccurrenceSearch(baseUrl);
|
||||
}catch (Exception e) {
|
||||
logger.error("error contacting gbif server");
|
||||
writer.write(new StreamBlockingException(Constants.REPOSITORY_NAME));
|
||||
return;
|
||||
}
|
||||
while (keys.hasNext()){
|
||||
String key = keys.next();
|
||||
try{
|
||||
occSearch.searchByKey(writer, key, Constants.QUERY_LIMIT);
|
||||
}catch (Exception e) {
|
||||
logger.warn("error retrieving key "+key, e);
|
||||
writer.write(new StreamNonBlockingException(Constants.REPOSITORY_NAME,key));
|
||||
}
|
||||
}
|
||||
writer.close();
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
public void getOccurrencesByIds(ClosableWriter<OccurrencePoint> writer,
|
||||
Iterator<String> ids) {
|
||||
OccurrenceSearch occSearch = null;
|
||||
try{
|
||||
occSearch = new OccurrenceSearch(baseUrl);
|
||||
}catch (Exception e) {
|
||||
logger.error("error contacting gbif server");
|
||||
writer.write(new StreamBlockingException(Constants.REPOSITORY_NAME));
|
||||
return;
|
||||
}
|
||||
while (ids.hasNext()){
|
||||
String id = ids.next();
|
||||
try{
|
||||
if (!writer.isAlive()){
|
||||
logger.trace("the writer is closed");
|
||||
return;
|
||||
}else writer.write(occSearch.searchById(id));
|
||||
}catch (Exception e) {
|
||||
logger.warn("error retrieving id "+id,e);
|
||||
writer.write(new StreamNonBlockingException(Constants.REPOSITORY_NAME,id));
|
||||
}
|
||||
}
|
||||
writer.close();
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
@ -0,0 +1,43 @@
|
||||
package org.gcube.data.spd.gbifplugin.search;
|
||||
|
||||
import static org.gcube.data.spd.gbifplugin.search.query.MappingUtils.getAsString;
|
||||
|
||||
import java.util.Map;
|
||||
|
||||
import org.gcube.data.spd.gbifplugin.search.query.MappingUtils;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.QueryByIdentifier;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.QueryType;
|
||||
import org.gcube.data.spd.model.products.DataProvider;
|
||||
import org.gcube.data.spd.model.products.DataSet;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public class DataSetRetreiver {
|
||||
|
||||
private static Logger log = LoggerFactory.getLogger(DataSetRetreiver.class);
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
public static DataSet get(String key, String baseURL) throws Exception{
|
||||
long start = System.currentTimeMillis();
|
||||
QueryByIdentifier datasetQuery = new QueryByIdentifier(baseURL, key, QueryType.Dataset);
|
||||
Map<String, Object> mapping = MappingUtils.getObjectMapping(datasetQuery.build());
|
||||
DataSet dataset = new DataSet(key);
|
||||
dataset.setName(getAsString(mapping,"title"));
|
||||
dataset.setCitation(getAsString((Map<String, Object>)mapping.get("citation"),"text"));
|
||||
String providerKey = getAsString(mapping,"publishingOrganizationKey");
|
||||
dataset.setDataProvider(getDataProvider(providerKey, baseURL));
|
||||
log.trace("[Benchmark] time to retrieve dataset is "+(System.currentTimeMillis()-start));
|
||||
return dataset;
|
||||
}
|
||||
|
||||
private static DataProvider getDataProvider(String key, String baseURL) throws Exception{
|
||||
QueryByIdentifier datasetQuery = new QueryByIdentifier(baseURL, key, QueryType.Organization);
|
||||
Map<String, Object> mapping = MappingUtils.getObjectMapping(datasetQuery.build());
|
||||
|
||||
DataProvider dataProvider = new DataProvider(key);
|
||||
dataProvider.setName(getAsString(mapping, "title"));
|
||||
return dataProvider;
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,213 @@
|
||||
package org.gcube.data.spd.gbifplugin.search;
|
||||
|
||||
import static org.gcube.data.spd.gbifplugin.search.query.MappingUtils.getAsCalendar;
|
||||
import static org.gcube.data.spd.gbifplugin.search.query.MappingUtils.getAsDouble;
|
||||
import static org.gcube.data.spd.gbifplugin.search.query.MappingUtils.getAsInteger;
|
||||
import static org.gcube.data.spd.gbifplugin.search.query.MappingUtils.getAsString;
|
||||
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.Calendar;
|
||||
import java.util.HashMap;
|
||||
import java.util.LinkedList;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
import org.gcube.data.spd.gbifplugin.Constants;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.MappingUtils;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.PagedQueryIterator;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.PagedQueryObject;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.QueryByIdentifier;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.QueryCondition;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.QueryType;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.ResultType;
|
||||
import org.gcube.data.spd.model.BasisOfRecord;
|
||||
import org.gcube.data.spd.model.Condition;
|
||||
import org.gcube.data.spd.model.exceptions.StreamBlockingException;
|
||||
import org.gcube.data.spd.model.products.DataSet;
|
||||
import org.gcube.data.spd.model.products.OccurrencePoint;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ObjectWriter;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public class OccurrenceSearch {
|
||||
|
||||
private static Logger log = LoggerFactory.getLogger(OccurrenceSearch.class);
|
||||
|
||||
private String baseURL;
|
||||
|
||||
private final SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd");
|
||||
|
||||
public OccurrenceSearch(String baseURL) {
|
||||
this.baseURL = baseURL;
|
||||
}
|
||||
|
||||
public void search(ObjectWriter<OccurrencePoint> writer, String scientificName, int limit, Condition ...conditions) throws Exception{
|
||||
PagedQueryObject occurrencesQuery = new PagedQueryObject(baseURL, ResultType.Occurrence, limit);
|
||||
List<QueryCondition> queryConditions = Utils.elaborateConditions(conditions);
|
||||
occurrencesQuery.setConditions(QueryCondition.cond("scientificName",scientificName.replaceAll(" ", "%20")), QueryCondition.cond("hasCoordinate","true"));
|
||||
occurrencesQuery.getConditions().addAll(queryConditions);
|
||||
|
||||
writeElements(writer, occurrencesQuery, null);
|
||||
}
|
||||
|
||||
public void searchByKey(ObjectWriter<OccurrencePoint> writer, String key, int limit) throws Exception{
|
||||
PagedQueryObject occurrencesQuery = new PagedQueryObject(baseURL, ResultType.Occurrence, limit);
|
||||
ProductKey productKey = Utils.elaborateProductsKey(key);
|
||||
occurrencesQuery.getConditions().addAll(productKey.getQueryCondition());
|
||||
occurrencesQuery.getConditions().add( QueryCondition.cond("hasCoordinate","true"));
|
||||
writeElements(writer, occurrencesQuery, productKey.getDataset());
|
||||
}
|
||||
|
||||
private void writeElements(ObjectWriter<OccurrencePoint> writer, PagedQueryObject occurrencesQuery, final DataSet dataset){
|
||||
PagedQueryIterator<OccurrencePoint> pagedIterator = new PagedQueryIterator<OccurrencePoint>(occurrencesQuery) {
|
||||
|
||||
@Override
|
||||
protected OccurrencePoint getObject(Map<String, Object> mappedObject)
|
||||
throws Exception {
|
||||
OccurrencePoint op = retrieveElement(mappedObject);
|
||||
if (dataset!=null){
|
||||
Calendar now = Calendar.getInstance();
|
||||
String credits = "Biodiversity occurrence data published by: "+dataset.getDataProvider().getName()+" (Accessed through GBIF Data Portal, data.gbif.org, "+format.format(now.getTime())+")";
|
||||
op.setCredits(credits);
|
||||
op.setDataSet(dataset);
|
||||
}
|
||||
return op;
|
||||
}
|
||||
|
||||
};
|
||||
|
||||
try{
|
||||
while (pagedIterator.hasNext() && writer.isAlive())
|
||||
writer.write(pagedIterator.next());
|
||||
}catch(Exception e){
|
||||
log.error("error writing occurrences",e);
|
||||
writer.write(new StreamBlockingException(Constants.REPOSITORY_NAME));
|
||||
}
|
||||
}
|
||||
|
||||
public OccurrencePoint searchById(String id) throws Exception{
|
||||
QueryByIdentifier queryByIdentifier = new QueryByIdentifier(baseURL, id, QueryType.Occurrence);
|
||||
return retrieveElement(MappingUtils.getObjectMapping(queryByIdentifier.build()));
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
FOSSIL_SPECIMEN
|
||||
An occurrence record describing a fossilized specimen.
|
||||
HUMAN_OBSERVATION
|
||||
An occurrence record describing an observation made by one or more people.
|
||||
LITERATURE
|
||||
An occurrence record based on literature alone.
|
||||
LIVING_SPECIMEN
|
||||
An occurrence record describing a living specimen, e.g.
|
||||
MACHINE_OBSERVATION
|
||||
An occurrence record describing an observation made by a machine.
|
||||
MATERIAL_SAMPLE
|
||||
An occurrence record based on samples taken from other specimens or the environment.
|
||||
OBSERVATION
|
||||
An occurrence record describing an observation.
|
||||
PRESERVED_SPECIMEN
|
||||
An occurrence record describing a preserved specimen.
|
||||
UNKNOWN
|
||||
*/
|
||||
|
||||
private static BasisOfRecord matchBasisOfRecord(String value){
|
||||
if (value.equals("PRESERVED_SPECIMEN")) return BasisOfRecord.PreservedSpecimen;
|
||||
else if (value.equals("HUMAN_OBSERVATION")) return BasisOfRecord.HumanObservation;
|
||||
else if (value.equals("FOSSIL_SPECIMEN")) return BasisOfRecord.FossilSpecimen;
|
||||
else if (value.equals("MACHINE_OBSERVATION")) return BasisOfRecord.MachineObservation;
|
||||
else if (value.equals("LIVING_SPECIMEN")) return BasisOfRecord.LivingSpecimen;
|
||||
else if (value.equals("OBSERVATION")) return BasisOfRecord.Observation;
|
||||
else if (value.equals("MATERIAL_SAMPLE")) return BasisOfRecord.MaterialSample;
|
||||
else if (value.equals("LITERATURE")) return BasisOfRecord.Literature;
|
||||
return BasisOfRecord.Unknown;
|
||||
}
|
||||
|
||||
|
||||
|
||||
private OccurrencePoint retrieveElement(Map<String, Object> mappedObj) throws Exception{
|
||||
long start = System.currentTimeMillis();
|
||||
String occurrenceId = getAsInteger(mappedObj, "key").toString();
|
||||
OccurrencePoint occurrence = new OccurrencePoint(occurrenceId);
|
||||
|
||||
occurrence.setCollectionCode(getAsString(mappedObj, "collectionCode"));
|
||||
occurrence.setInstitutionCode(getAsString(mappedObj, "institutionCode"));
|
||||
occurrence.setCatalogueNumber(getAsString(mappedObj, "catalogNumber"));
|
||||
occurrence.setRecordedBy(getAsString(mappedObj, "recordedBy"));
|
||||
occurrence.setIdentifiedBy(getAsString(mappedObj, "identifiedBy"));
|
||||
occurrence.setCountry(getAsString(mappedObj, "country"));
|
||||
occurrence.setLocality(getAsString(mappedObj, "locality"));
|
||||
|
||||
Calendar eventDate = getAsCalendar(mappedObj, "eventDate");
|
||||
if (eventDate==null)
|
||||
eventDate =getAsCalendar(mappedObj,"dateIdentified");
|
||||
|
||||
occurrence.setEventDate(eventDate);
|
||||
|
||||
occurrence.setDecimalLatitude(getAsDouble(mappedObj, "decimalLatitude"));
|
||||
occurrence.setDecimalLongitude(getAsDouble(mappedObj, "decimalLongitude"));
|
||||
|
||||
occurrence.setBasisOfRecord(matchBasisOfRecord(getAsString(mappedObj, "basisOfRecord")));
|
||||
|
||||
occurrence.setMinDepth(getAsDouble(mappedObj, "elevation"));
|
||||
occurrence.setMaxDepth(getAsDouble(mappedObj, "depth"));
|
||||
|
||||
String taxonKey = getAsInteger(mappedObj, "taxonKey").toString();
|
||||
ReducedTaxon rt = retrieveParentTaxon(taxonKey);
|
||||
occurrence.setKingdom(rt.getKingdom());
|
||||
occurrence.setFamily(rt.getFamily());
|
||||
|
||||
QueryByIdentifier taxonQuery = new QueryByIdentifier(baseURL, taxonKey , QueryType.Taxon);
|
||||
Map<String, Object> taxon = MappingUtils.getObjectMapping(taxonQuery.build());
|
||||
occurrence.setScientificNameAuthorship(getAsString(taxon, "authorship"));
|
||||
occurrence.setScientificName(getAsString(taxon, "scientificName"));
|
||||
occurrence.setCitation(getAsString(taxon, "accordingTo"));
|
||||
log.trace("[Benchmark] time to retrieve occurrence is "+(System.currentTimeMillis()-start));
|
||||
return occurrence;
|
||||
}
|
||||
|
||||
|
||||
private ReducedTaxon retrieveParentTaxon(String taxonId) throws Exception {
|
||||
long start = System.currentTimeMillis();
|
||||
QueryByIdentifier query = new QueryByIdentifier(baseURL, taxonId, QueryType.Taxon);
|
||||
query.addPath("parents");
|
||||
LinkedList<HashMap<String, Object>> parentsList = MappingUtils.getObjectList(query.build());
|
||||
ReducedTaxon taxon = new ReducedTaxon();
|
||||
for(HashMap<String, Object> mappedObject : parentsList){
|
||||
String rank = getAsString(mappedObject, "rank");
|
||||
String value = getAsString(mappedObject, "scientificName");
|
||||
if (rank.equalsIgnoreCase("family"))
|
||||
taxon.setFamily(value);
|
||||
else if (rank.equalsIgnoreCase("kingdom"))
|
||||
taxon.setKingdom(value);
|
||||
if (taxon.isValid())
|
||||
return taxon;
|
||||
}
|
||||
log.trace("[Benchmark] time to retrieve taxon is "+(System.currentTimeMillis()-start));
|
||||
return taxon;
|
||||
}
|
||||
|
||||
|
||||
protected static class ReducedTaxon{
|
||||
|
||||
private String family = null;
|
||||
private String kingdom = null;
|
||||
public String getFamily() {
|
||||
return family;
|
||||
}
|
||||
public void setFamily(String family) {
|
||||
this.family = family;
|
||||
}
|
||||
public String getKingdom() {
|
||||
return kingdom;
|
||||
}
|
||||
public void setKingdom(String kingdom) {
|
||||
this.kingdom = kingdom;
|
||||
}
|
||||
|
||||
public boolean isValid(){
|
||||
return family!=null && kingdom!=null;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,20 @@
|
||||
package org.gcube.data.spd.gbifplugin.search;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
import lombok.AllArgsConstructor;
|
||||
import lombok.Getter;
|
||||
|
||||
import org.gcube.data.spd.gbifplugin.search.query.QueryCondition;
|
||||
import org.gcube.data.spd.model.products.DataSet;
|
||||
|
||||
@AllArgsConstructor
|
||||
@Getter
|
||||
public class ProductKey {
|
||||
|
||||
private List<QueryCondition> queryCondition;
|
||||
private DataSet dataset;
|
||||
|
||||
|
||||
|
||||
}
|
||||
@ -0,0 +1,159 @@
|
||||
package org.gcube.data.spd.gbifplugin.search;
|
||||
|
||||
import static org.gcube.data.spd.gbifplugin.search.query.MappingUtils.getAsString;
|
||||
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.Calendar;
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.LinkedList;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Set;
|
||||
|
||||
import org.gcube.data.spd.gbifplugin.Constants;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.MappingUtils;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.PagedQueryIterator;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.PagedQueryObject;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.QueryByIdentifier;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.QueryCondition;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.QueryCount;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.QueryType;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.ResultType;
|
||||
import org.gcube.data.spd.model.Condition;
|
||||
import org.gcube.data.spd.model.exceptions.StreamBlockingException;
|
||||
import org.gcube.data.spd.model.products.DataSet;
|
||||
import org.gcube.data.spd.model.products.Product;
|
||||
import org.gcube.data.spd.model.products.Product.ProductType;
|
||||
import org.gcube.data.spd.model.products.ResultItem;
|
||||
import org.gcube.data.spd.model.products.Taxon;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ObjectWriter;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public class ResultItemSearch {
|
||||
|
||||
private static final SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd");
|
||||
|
||||
private static Logger log = LoggerFactory.getLogger(ResultItemSearch.class);
|
||||
|
||||
private List<QueryCondition> queryConditions = new ArrayList<QueryCondition>();
|
||||
|
||||
private String baseURL;
|
||||
|
||||
String searchQuery;
|
||||
|
||||
public ResultItemSearch(String baseURL, String searchQuery, Condition ... conditions){
|
||||
this.baseURL = baseURL;
|
||||
this.searchQuery = searchQuery.replaceAll(" ", "%20");
|
||||
try{
|
||||
this.queryConditions = Utils.elaborateConditions(conditions);
|
||||
}catch(Exception e){
|
||||
log.error("error elaborating conditions",e);
|
||||
}
|
||||
}
|
||||
|
||||
public void search(ObjectWriter<ResultItem> writer, int limit){
|
||||
PagedQueryObject queryObject = new PagedQueryObject(baseURL, ResultType.Occurrence,limit);
|
||||
queryObject.setConditions(QueryCondition.cond("scientificName",searchQuery));
|
||||
try{
|
||||
PagedQueryIterator<ResultItem> pagedIterator = new PagedQueryIterator<ResultItem>(queryObject) {
|
||||
|
||||
Set<String> alreadyVisited =new HashSet<String>();
|
||||
|
||||
@Override
|
||||
protected ResultItem getObject(Map<String, Object> mappedObject) throws Exception {
|
||||
return buildResult(mappedObject);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected boolean useIt(Map<String, Object> mappedObject) {
|
||||
String datasetKey = getAsString(mappedObject,"datasetKey");
|
||||
Integer taxonId = (Integer)mappedObject.get("taxonKey");
|
||||
String key = datasetKey+"|"+taxonId;
|
||||
if (alreadyVisited.contains(key))
|
||||
return false;
|
||||
alreadyVisited.add(key);
|
||||
return true;
|
||||
}
|
||||
|
||||
};
|
||||
|
||||
while (pagedIterator.hasNext() && writer.isAlive())
|
||||
writer.write(pagedIterator.next());
|
||||
|
||||
}catch(Exception e){
|
||||
log.error("error writing resultItems",e);
|
||||
writer.write(new StreamBlockingException(Constants.REPOSITORY_NAME));
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
ResultItem buildResult(Map<String,Object> singleObject) throws Exception{
|
||||
long start = System.currentTimeMillis();
|
||||
Integer taxonId = (Integer)singleObject.get("taxonKey");
|
||||
String scientificName = getAsString(singleObject,"species");
|
||||
ResultItem resItem = new ResultItem(taxonId.toString(), scientificName );
|
||||
|
||||
resItem.setParent(retrieveTaxon(taxonId.toString()));
|
||||
|
||||
resItem.setScientificNameAuthorship(retrieveAuthorship(taxonId.toString()));
|
||||
|
||||
resItem.setRank(getAsString(singleObject, "taxonRank"));
|
||||
|
||||
resItem.setCitation(getAsString(singleObject,"institutionCode"));
|
||||
|
||||
DataSet dataset = DataSetRetreiver.get(getAsString(singleObject,"datasetKey"), baseURL);
|
||||
resItem.setDataSet(dataset);
|
||||
|
||||
List<Product> products = retrieveProducts(taxonId.toString(), dataset);
|
||||
resItem.setProducts(products);
|
||||
|
||||
String credits = "Biodiversity occurrence data published by: "+dataset.getDataProvider().getName()+" (Accessed through GBIF Data Portal, data.gbif.org, "+format.format(Calendar.getInstance().getTime())+")";
|
||||
resItem.setCredits(credits);
|
||||
log.trace("[Benchmark] time to retrieve ResultItem is "+(System.currentTimeMillis()-start));
|
||||
return resItem;
|
||||
}
|
||||
|
||||
private String retrieveAuthorship(String taxonId) throws Exception {
|
||||
QueryByIdentifier query = new QueryByIdentifier(baseURL, taxonId, QueryType.Taxon);
|
||||
Map<String, Object> mapping = MappingUtils.getObjectMapping(query.build());
|
||||
if (mapping.containsKey("authorship"))
|
||||
return getAsString(mapping, "authorship");
|
||||
else return "";
|
||||
}
|
||||
|
||||
private Taxon retrieveTaxon(String taxonId) throws Exception {
|
||||
long start = System.currentTimeMillis();
|
||||
QueryByIdentifier query = new QueryByIdentifier(baseURL, taxonId, QueryType.Taxon);
|
||||
query.addPath("parents");
|
||||
LinkedList<HashMap<String, Object>> parentsList = MappingUtils.getObjectList(query.build());
|
||||
Taxon parentTaxon = null;
|
||||
for(HashMap<String, Object> mappedObject : parentsList){
|
||||
Taxon taxon = new Taxon(((Integer)mappedObject.get("key")).toString(), getAsString(mappedObject, "scientificName"));
|
||||
taxon.setCitation(getAsString(mappedObject, "accordingTo"));
|
||||
taxon.setRank(getAsString(mappedObject, "rank"));
|
||||
if (parentTaxon!=null)
|
||||
taxon.setParent(parentTaxon);
|
||||
parentTaxon = taxon;
|
||||
}
|
||||
log.trace("[Benchmark] time to retrieve taxon is "+(System.currentTimeMillis()-start));
|
||||
return parentTaxon;
|
||||
}
|
||||
|
||||
private List<Product> retrieveProducts( String taxonId, DataSet dataset, Condition ... properties) throws Exception{
|
||||
long start = System.currentTimeMillis();
|
||||
QueryCount occurrencesQuery = new QueryCount(baseURL, ResultType.Occurrence);
|
||||
occurrencesQuery.setConditions(QueryCondition.cond("taxonKey",taxonId), QueryCondition.cond("datasetKey", dataset.getId()), QueryCondition.cond("hasCoordinate","true"));
|
||||
String productId = Utils.createProductsKey(Utils.getDataSetAsString(dataset), taxonId, this.queryConditions);
|
||||
Product product = new Product(ProductType.Occurrence, productId);
|
||||
product.setCount(occurrencesQuery.getCount());
|
||||
log.trace("[Benchmark] time to retrieve product is "+(System.currentTimeMillis()-start));
|
||||
return Arrays.asList(product);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
@ -0,0 +1,136 @@
|
||||
package org.gcube.data.spd.gbifplugin.search;
|
||||
|
||||
import static org.gcube.data.spd.gbifplugin.search.query.QueryCondition.cond;
|
||||
|
||||
import java.text.DateFormat;
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Calendar;
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.data.spd.gbifplugin.search.query.QueryCondition;
|
||||
import org.gcube.data.spd.model.Condition;
|
||||
import org.gcube.data.spd.model.Coordinate;
|
||||
import org.gcube.data.spd.model.products.DataProvider;
|
||||
import org.gcube.data.spd.model.products.DataSet;
|
||||
|
||||
public class Utils {
|
||||
|
||||
protected static List<QueryCondition> elaborateConditions(Condition[] properties) throws Exception{
|
||||
List<QueryCondition> queryConditions = new ArrayList<QueryCondition>();
|
||||
for (Condition prop: properties){
|
||||
switch (prop.getType()) {
|
||||
case COORDINATE:
|
||||
Coordinate coord = (Coordinate)prop.getValue();
|
||||
queryConditions.addAll(getCoordinateConditions(coord, prop));
|
||||
break;
|
||||
case DATE:
|
||||
Calendar date = (Calendar) prop.getValue();
|
||||
queryConditions.addAll(getDateCondition(date, prop));
|
||||
break;
|
||||
}
|
||||
}
|
||||
return queryConditions;
|
||||
}
|
||||
|
||||
public static ProductKey elaborateProductsKey(String id) {
|
||||
List<QueryCondition> queryConditions = new ArrayList<QueryCondition>();
|
||||
String[] splitString = id.split("\\|\\|");
|
||||
|
||||
DataSet dataset = getDataSetFromString(splitString[0]);
|
||||
queryConditions.add(cond("datasetKey", dataset.getId()));
|
||||
queryConditions.add(cond("taxonKey", splitString[1]));
|
||||
if (splitString.length>2)
|
||||
for (int i = 2; i<=splitString.length; i++){
|
||||
String[] equalSplit = splitString[i].split("=");
|
||||
queryConditions.add(cond(equalSplit[0], equalSplit[1]));
|
||||
}
|
||||
return new ProductKey(queryConditions, dataset);
|
||||
}
|
||||
|
||||
protected static String createProductsKey(String dataResourceKey, String taxonKey, List<QueryCondition> queryConditions) {
|
||||
StringBuilder conditionTransformer = new StringBuilder();
|
||||
for (QueryCondition cond : queryConditions)
|
||||
conditionTransformer.append("||").append(cond.getKey()).append("=").append(cond.getValue());
|
||||
return dataResourceKey+"||"+taxonKey+conditionTransformer.toString();
|
||||
}
|
||||
|
||||
public static List<QueryCondition> getCoordinateConditions(Coordinate coordinate, Condition prop){
|
||||
List<QueryCondition> conditions = new ArrayList<QueryCondition>();
|
||||
switch (prop.getOp()) {
|
||||
case EQ:
|
||||
conditions.add(cond("decimalLatitiude",coordinate.getLatitude()+""));
|
||||
conditions.add(cond("decimalLongitude",coordinate.getLongitude()+""));
|
||||
break;
|
||||
case GT:
|
||||
conditions.add(cond("decimalLatitiude",(coordinate.getLatitude()+0.01)+",90"));
|
||||
conditions.add(cond("decimalLongitude",(coordinate.getLongitude()+0.01)+",180"));
|
||||
break;
|
||||
case GE:
|
||||
conditions.add(cond("decimalLatitiude",coordinate.getLatitude()+",90"));
|
||||
conditions.add(cond("decimalLongitude",coordinate.getLongitude()+",180"));
|
||||
break;
|
||||
case LT:
|
||||
conditions.add(cond("decimalLatitiude","-90,"+(coordinate.getLatitude()+0.01)));
|
||||
conditions.add(cond("decimalLongitude","-180,"+(coordinate.getLongitude()+0.01)));
|
||||
break;
|
||||
case LE:
|
||||
conditions.add(cond("decimalLatitiude","-90,"+coordinate.getLatitude()));
|
||||
conditions.add(cond("decimalLongitude","-180,"+coordinate.getLongitude()));
|
||||
break;
|
||||
default:
|
||||
break;
|
||||
}
|
||||
return conditions;
|
||||
}
|
||||
|
||||
public static List<QueryCondition> getDateCondition(Calendar date, Condition prop){
|
||||
List<QueryCondition> conditions = new ArrayList<QueryCondition>();
|
||||
DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd");
|
||||
Calendar newDate = date;
|
||||
Calendar now = Calendar.getInstance();
|
||||
switch (prop.getOp()) {
|
||||
case EQ:
|
||||
conditions.add(cond("eventDate",dateFormat.format(date.getTime())));
|
||||
break;
|
||||
case GT:
|
||||
newDate.add(Calendar.DAY_OF_MONTH, -1);
|
||||
conditions.add(cond("eventDate",dateFormat.format(date.getTime())+","+dateFormat.format(now.getTime())));
|
||||
break;
|
||||
case GE:
|
||||
conditions.add(cond("eventDate",dateFormat.format(date.getTime())+","+dateFormat.format(now.getTime())));
|
||||
break;
|
||||
case LT:
|
||||
newDate.add(Calendar.DAY_OF_MONTH, 1);
|
||||
conditions.add(cond("eventDate","1000-01-01,"+dateFormat.format(now.getTime())));
|
||||
break;
|
||||
case LE:
|
||||
conditions.add(cond("eventDate","1000-01-01,"+dateFormat.format(now.getTime())));
|
||||
break;
|
||||
default:
|
||||
break;
|
||||
}
|
||||
return conditions;
|
||||
}
|
||||
|
||||
protected static String getDataSetAsString(DataSet dataset){
|
||||
StringBuilder datasetAsString = new StringBuilder(
|
||||
dataset.getId())
|
||||
.append("^^").append(dataset.getName())
|
||||
.append("^^").append(dataset.getCitation())
|
||||
.append("^^").append(dataset.getDataProvider().getId())
|
||||
.append("^^").append(dataset.getDataProvider().getName());
|
||||
return datasetAsString.toString();
|
||||
}
|
||||
|
||||
protected static DataSet getDataSetFromString(String datasetString){
|
||||
String[] splittedDataset = datasetString.split("\\^\\^");
|
||||
DataSet dataset = new DataSet(splittedDataset[0]);
|
||||
dataset.setName(splittedDataset[1]);
|
||||
dataset.setCitation(splittedDataset[2]);
|
||||
DataProvider dataProvider = new DataProvider(splittedDataset[3]);
|
||||
dataProvider.setName(splittedDataset[4]);
|
||||
dataset.setDataProvider(dataProvider);
|
||||
return dataset;
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,85 @@
|
||||
package org.gcube.data.spd.gbifplugin.search.query;
|
||||
|
||||
import java.io.StringReader;
|
||||
import java.text.DateFormat;
|
||||
import java.text.ParseException;
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.Calendar;
|
||||
import java.util.HashMap;
|
||||
import java.util.LinkedList;
|
||||
import java.util.Locale;
|
||||
import java.util.Map;
|
||||
|
||||
import javax.ws.rs.core.MediaType;
|
||||
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.core.type.TypeReference;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.sun.jersey.api.client.Client;
|
||||
import com.sun.jersey.api.client.WebResource;
|
||||
import com.sun.jersey.api.client.config.ClientConfig;
|
||||
import com.sun.jersey.api.client.config.DefaultClientConfig;
|
||||
|
||||
public class MappingUtils {
|
||||
|
||||
private static Logger log = LoggerFactory.getLogger(MappingUtils.class);
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
public static Map<String, Object> getObjectMapping(String query) throws Exception{
|
||||
ClientConfig clientConfig = new DefaultClientConfig();
|
||||
Client client = Client.create(clientConfig);
|
||||
WebResource target = client.resource(query);
|
||||
//NameUsageWsClient nuws = new NameUsageWsClient(target);
|
||||
String response = target.type(MediaType.APPLICATION_JSON).acceptLanguage(Locale.ENGLISH).get(String.class);
|
||||
ObjectMapper mapper = new ObjectMapper(); // can reuse, share globally
|
||||
return mapper.readValue(new StringReader(response), Map.class);
|
||||
|
||||
}
|
||||
|
||||
public static LinkedList<HashMap<String, Object>> getObjectList(String query) throws Exception{
|
||||
ClientConfig clientConfig = new DefaultClientConfig();
|
||||
Client client = Client.create(clientConfig);
|
||||
WebResource target = client.resource(query);
|
||||
//NameUsageWsClient nuws = new NameUsageWsClient(target);
|
||||
String response = target.type(MediaType.APPLICATION_JSON).acceptLanguage(Locale.ENGLISH).get(String.class);
|
||||
ObjectMapper mapper = new ObjectMapper(); // can reuse, share globally
|
||||
return mapper.readValue(new StringReader(response), new TypeReference<LinkedList<HashMap<String, Object>>>() {
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
public static String getAsString(Map<String, Object> map, String key){
|
||||
if (!map.containsKey(key)) return null;
|
||||
return (String) map.get(key);
|
||||
}
|
||||
|
||||
public static Double getAsDouble(Map<String, Object> map, String key){
|
||||
if (!map.containsKey(key)) return 0d;
|
||||
return (Double) map.get(key);
|
||||
}
|
||||
|
||||
public static Integer getAsInteger(Map<String, Object> map, String key){
|
||||
if (!map.containsKey(key)) return 0;
|
||||
return (Integer) map.get(key);
|
||||
}
|
||||
|
||||
public static Calendar getAsCalendar(Map<String, Object> map, String key){
|
||||
if (!map.containsKey(key)) return null;
|
||||
return parseCalendar((String) map.get(key));
|
||||
}
|
||||
|
||||
|
||||
public static Calendar parseCalendar(String date){
|
||||
try{
|
||||
DateFormat df = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSSZ");
|
||||
Calendar calendar= Calendar.getInstance();
|
||||
calendar.setTime(df.parse(date));
|
||||
return calendar;
|
||||
}catch (ParseException e) {
|
||||
log.warn("DateModified discarded ("+date+")");
|
||||
return null;
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,85 @@
|
||||
package org.gcube.data.spd.gbifplugin.search.query;
|
||||
|
||||
import java.util.Iterator;
|
||||
import java.util.Map;
|
||||
|
||||
import lombok.NonNull;
|
||||
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public abstract class PagedQueryIterator<T> implements Iterator<T>{
|
||||
|
||||
private static Logger log = LoggerFactory.getLogger(PagedQueryIterator.class);
|
||||
|
||||
private @NonNull PagedQueryObject pagedQuery;
|
||||
|
||||
public PagedQueryIterator(@NonNull PagedQueryObject pagedQuery) {
|
||||
this.pagedQuery = pagedQuery;
|
||||
}
|
||||
|
||||
protected abstract T getObject(Map<String,Object> mappedObject) throws Exception;
|
||||
|
||||
Map<String, Object> mapping;
|
||||
|
||||
Iterator<Map<String,Object>> resultIterator;
|
||||
|
||||
Map<String,Object> actualObject= null;
|
||||
|
||||
Long start = null;
|
||||
Long parsingStart = null;
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
@Override
|
||||
public boolean hasNext() {
|
||||
try{
|
||||
if (resultIterator==null){
|
||||
String query = pagedQuery.buildNext();
|
||||
start = System.currentTimeMillis();
|
||||
mapping = MappingUtils.getObjectMapping(query);
|
||||
parsingStart = System.currentTimeMillis();
|
||||
log.trace("[Benchmark] got Elements with query "+query+" and took "+(parsingStart-start));
|
||||
resultIterator = ((Iterable<Map<String,Object>>) mapping.get("results")).iterator();
|
||||
}
|
||||
|
||||
if (!resultIterator.hasNext()){
|
||||
log.trace("[Benchmark] page retrieved and parsed in "+(System.currentTimeMillis()-start));
|
||||
if ((Boolean)mapping.get("endOfRecords")){
|
||||
log.trace("is end of records, no next element");
|
||||
return false;
|
||||
}
|
||||
resultIterator = null;
|
||||
|
||||
} else{
|
||||
actualObject = resultIterator.next();
|
||||
if (useIt(actualObject))
|
||||
return true;
|
||||
}
|
||||
return this.hasNext();
|
||||
|
||||
}catch(Exception e){
|
||||
log.error("error computing hasNext",e);
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public T next() {
|
||||
try{
|
||||
return getObject(actualObject);
|
||||
}catch(Exception e){
|
||||
log.error("error computing next",e);
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
protected boolean useIt(Map<String,Object> mappedObject){
|
||||
return true;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void remove() {
|
||||
resultIterator = null;
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,47 @@
|
||||
package org.gcube.data.spd.gbifplugin.search.query;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import lombok.Getter;
|
||||
import lombok.NonNull;
|
||||
import lombok.RequiredArgsConstructor;
|
||||
|
||||
|
||||
@RequiredArgsConstructor
|
||||
public class PagedQueryObject {
|
||||
|
||||
private @NonNull String baseUri;
|
||||
|
||||
@Getter
|
||||
List<QueryCondition> conditions = new ArrayList<QueryCondition>();
|
||||
|
||||
private @NonNull ResultType resultType;
|
||||
|
||||
private @NonNull Integer resultPerQuery;
|
||||
|
||||
private int offset = 0;
|
||||
|
||||
public void setConditions(QueryCondition ... conditions){
|
||||
this.conditions = Arrays.asList(conditions);
|
||||
}
|
||||
|
||||
|
||||
|
||||
public String buildNext(){
|
||||
StringBuilder query = new StringBuilder(baseUri);
|
||||
if (!baseUri.endsWith("/")) query.append("/");
|
||||
query.append(this.resultType.getQueryEntry()).append("/");
|
||||
query.append("search/?limit=").append(resultPerQuery);
|
||||
query.append("&offset=").append(offset);
|
||||
|
||||
if (conditions.size()>0)
|
||||
for (QueryCondition queryCond: conditions)
|
||||
query.append("&").append(queryCond.getKey()).append("=").append(queryCond.getValue());
|
||||
offset = offset+resultPerQuery;
|
||||
return query.toString();
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
@ -0,0 +1,35 @@
|
||||
package org.gcube.data.spd.gbifplugin.search.query;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import lombok.NonNull;
|
||||
import lombok.RequiredArgsConstructor;
|
||||
|
||||
@RequiredArgsConstructor
|
||||
public class QueryByIdentifier {
|
||||
|
||||
private @NonNull String baseUri;
|
||||
|
||||
private @NonNull String key;
|
||||
|
||||
private @NonNull QueryType type;
|
||||
|
||||
private List<String> paths = new ArrayList<String>();
|
||||
|
||||
public void addPath(String path){
|
||||
paths.add(path);
|
||||
}
|
||||
|
||||
public String build(){
|
||||
StringBuilder query = new StringBuilder(baseUri);
|
||||
if (!baseUri.endsWith("/")) query.append("/");
|
||||
query.append(this.type.getQueryEntry()).append("/");
|
||||
query.append(key);
|
||||
for (String path : paths)
|
||||
query.append("/").append(path);
|
||||
return query.toString();
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
@ -0,0 +1,20 @@
|
||||
package org.gcube.data.spd.gbifplugin.search.query;
|
||||
|
||||
import lombok.Getter;
|
||||
import lombok.NonNull;
|
||||
import lombok.RequiredArgsConstructor;
|
||||
|
||||
|
||||
@RequiredArgsConstructor
|
||||
public class QueryCondition{
|
||||
|
||||
public static QueryCondition cond(String key, String value){
|
||||
return new QueryCondition(key, value);
|
||||
}
|
||||
|
||||
@Getter
|
||||
private @NonNull String key;
|
||||
@Getter
|
||||
private @NonNull String value;
|
||||
|
||||
}
|
||||
@ -0,0 +1,54 @@
|
||||
package org.gcube.data.spd.gbifplugin.search.query;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
import lombok.NonNull;
|
||||
import lombok.RequiredArgsConstructor;
|
||||
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
@RequiredArgsConstructor
|
||||
public class QueryCount {
|
||||
|
||||
private static Logger log = LoggerFactory.getLogger(QueryCount.class);
|
||||
|
||||
private @NonNull String baseUri;
|
||||
|
||||
List<QueryCondition> conditions = new ArrayList<QueryCondition>();
|
||||
|
||||
private @NonNull ResultType resultType;
|
||||
|
||||
public void setConditions(QueryCondition ... conditions){
|
||||
this.conditions = Arrays.asList(conditions);
|
||||
}
|
||||
|
||||
public int getCount(){
|
||||
Map<String, Object> mapping;
|
||||
try {
|
||||
mapping = MappingUtils.getObjectMapping(this.build());
|
||||
if (mapping.get("count")==null) return 0;
|
||||
return (Integer)mapping.get("count");
|
||||
} catch (Exception e) {
|
||||
log.error("error computing count, returning 0",e);
|
||||
return 0;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
private String build(){
|
||||
StringBuilder query = new StringBuilder(baseUri);
|
||||
if (!baseUri.endsWith("/")) query.append("/");
|
||||
query.append(this.resultType.getQueryEntry()).append("/");
|
||||
query.append("search/?limit=0");
|
||||
|
||||
if (conditions.size()>0)
|
||||
for (QueryCondition queryCond: conditions)
|
||||
query.append("&").append(queryCond.getKey().replaceAll(" ", "%20")).append("=").append(queryCond.getValue().replaceAll(" ", "%20"));
|
||||
return query.toString();
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,17 @@
|
||||
package org.gcube.data.spd.gbifplugin.search.query;
|
||||
|
||||
import lombok.AllArgsConstructor;
|
||||
import lombok.Getter;
|
||||
import lombok.NonNull;
|
||||
|
||||
|
||||
public @AllArgsConstructor enum QueryType{
|
||||
Dataset("dataset"),
|
||||
Occurrence("occurrence"),
|
||||
Taxon("species"),
|
||||
Organization("organization");
|
||||
|
||||
@Getter
|
||||
private @NonNull String queryEntry;
|
||||
|
||||
}
|
||||
@ -0,0 +1,15 @@
|
||||
package org.gcube.data.spd.gbifplugin.search.query;
|
||||
|
||||
import lombok.Getter;
|
||||
import lombok.NonNull;
|
||||
import lombok.RequiredArgsConstructor;
|
||||
|
||||
@RequiredArgsConstructor
|
||||
public enum ResultType{
|
||||
Occurrence("occurrence"),
|
||||
Taxon("species");
|
||||
|
||||
@Getter
|
||||
private @NonNull String queryEntry;
|
||||
|
||||
}
|
||||
@ -0,0 +1 @@
|
||||
org.gcube.data.spd.gbifplugin.GBIFPlugin
|
||||
@ -0,0 +1,139 @@
|
||||
package org.gcube.data.spd.gbif;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.io.StringReader;
|
||||
import java.text.DateFormat;
|
||||
import java.text.ParseException;
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.Calendar;
|
||||
import java.util.Locale;
|
||||
import java.util.Map;
|
||||
import java.util.Map.Entry;
|
||||
|
||||
import javax.ws.rs.core.MediaType;
|
||||
|
||||
import org.gcube.data.spd.gbifplugin.search.OccurrenceSearch;
|
||||
import org.gcube.data.spd.gbifplugin.search.ResultItemSearch;
|
||||
import org.gcube.data.spd.gbifplugin.search.Utils;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.MappingUtils;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.PagedQueryIterator;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.PagedQueryObject;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.QueryCondition;
|
||||
import org.gcube.data.spd.gbifplugin.search.query.ResultType;
|
||||
import org.gcube.data.spd.model.exceptions.StreamException;
|
||||
import org.gcube.data.spd.model.products.OccurrencePoint;
|
||||
import org.gcube.data.spd.model.products.ResultItem;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ObjectWriter;
|
||||
import org.junit.Test;
|
||||
|
||||
import com.fasterxml.jackson.core.JsonParseException;
|
||||
import com.fasterxml.jackson.databind.JsonMappingException;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.sun.jersey.api.client.Client;
|
||||
import com.sun.jersey.api.client.WebResource;
|
||||
import com.sun.jersey.api.client.config.ClientConfig;
|
||||
import com.sun.jersey.api.client.config.DefaultClientConfig;
|
||||
|
||||
|
||||
public class QueryTest {
|
||||
|
||||
public static final String BASE_URL = "http://api.gbif.org/v1";
|
||||
|
||||
@Test
|
||||
public void query4Occurrence(){
|
||||
PagedQueryObject qo = new PagedQueryObject("http://api.gbif.org/v1/", ResultType.Occurrence, 50);
|
||||
qo.setConditions(QueryCondition.cond("scientificName","Palinurus%20elephas"), QueryCondition.cond("hasCoordinate","true"));
|
||||
PagedQueryIterator<String> pagedQuery = new PagedQueryIterator<String>(qo) {
|
||||
|
||||
@Override
|
||||
protected String getObject(Map<String, Object> mappedObject)
|
||||
throws Exception {
|
||||
System.out.println(mappedObject.toString());
|
||||
return mappedObject.toString();
|
||||
}
|
||||
};
|
||||
|
||||
while (pagedQuery.hasNext())
|
||||
System.out.println(pagedQuery.next());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void query4Taxon() throws JsonParseException, JsonMappingException, IOException{
|
||||
ClientConfig clientConfig = new DefaultClientConfig();
|
||||
Client client = Client.create(clientConfig);
|
||||
|
||||
WebResource target = client.resource("http://api.gbif.org/v1/species/search/?limit=1&offset=0&q=sarda%20sarda");
|
||||
|
||||
//NameUsageWsClient nuws = new NameUsageWsClient(target);
|
||||
String response = target.type(MediaType.APPLICATION_JSON).acceptLanguage(Locale.ENGLISH).get(String.class);
|
||||
ObjectMapper mapper = new ObjectMapper(); // can reuse, share globally
|
||||
Map<String,Object> userData = mapper.readValue(new StringReader(response), Map.class);
|
||||
for (Entry<String, Object> entry : userData.entrySet())
|
||||
System.out.println(String.format("entry name %s class value %s", entry.getKey(), entry.getValue().getClass().getSimpleName()));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void searchItems() throws Exception{
|
||||
|
||||
ResultItemSearch searcher = new ResultItemSearch(BASE_URL,"Limanda limanda");
|
||||
|
||||
searcher.search(new ObjectWriter<ResultItem>() {
|
||||
|
||||
int i =0;
|
||||
|
||||
@Override
|
||||
public boolean write(StreamException error) {
|
||||
error.printStackTrace();
|
||||
return false;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean write(ResultItem t) {
|
||||
System.out.println("written element "+(++i));
|
||||
return true;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean isAlive() {
|
||||
return true;
|
||||
}
|
||||
}, 50);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void searchOccurrences() throws Exception{
|
||||
|
||||
OccurrenceSearch searcher = new OccurrenceSearch(BASE_URL);
|
||||
|
||||
searcher.search(new ObjectWriter<OccurrencePoint>() {
|
||||
|
||||
int i =0;
|
||||
|
||||
@Override
|
||||
public boolean write(StreamException error) {
|
||||
error.printStackTrace();
|
||||
return false;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean write(OccurrencePoint t) {
|
||||
System.out.println("written element "+(++i));
|
||||
return true;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean isAlive() {
|
||||
return true;
|
||||
}
|
||||
}, "Limanda limanda", 50);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void dataTest() throws Exception{
|
||||
Utils.elaborateProductsKey("197908d0-5565-11d8-b290-b8a03c50a862^^Fishbase^^FishBase: Fishbase^^192a9ab0-5565-11d8-b290-b8a03c50a862^^FishBase||5208593");
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,10 @@
|
||||
log4j.appender.ROOT=org.apache.log4j.ConsoleAppender
|
||||
log4j.appender.ROOT.layout=org.apache.log4j.PatternLayout
|
||||
log4j.appender.ROOT.layout.ConversionPattern=%d{HH:mm:ss,SSS} %-5p %c{2} [%t,%M:%L] %m%n
|
||||
log4j.rootLogger=INFO,ROOT
|
||||
|
||||
log4j.appender.SPD-CL=org.apache.log4j.ConsoleAppender
|
||||
log4j.appender.SPD-CL.layout=org.apache.log4j.PatternLayout
|
||||
log4j.appender.SPD-CL.layout.ConversionPattern=[SPD-CL] %d{HH:mm:ss,SSS} %-5p %c{2} [%t,%M:%L] %m%n
|
||||
|
||||
log4j.category.org.gcube.data.spd=TRACE,SPD-CL
|
||||
Loading…
Reference in New Issue