release 4.3
git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/branches/data-access/spd-plugin-fwk/3.1@142009 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
commit
50c8d4ac0e
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@ -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/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
|
||||
<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>spd-plugin-framework</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 @@
|
|||
#Fri Jul 06 17:13:26 CEST 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 @@
|
|||
#Fri Jul 06 17:13:26 CEST 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 @@
|
|||
#Fri Jul 06 17:04:03 CEST 2012
|
||||
activeProfiles=
|
||||
eclipse.preferences.version=1
|
||||
resolveWorkspaceProjects=true
|
||||
version=1
|
||||
|
|
@ -0,0 +1 @@
|
|||
Used as a Library in the gCube Framework
|
||||
|
|
@ -0,0 +1,6 @@
|
|||
gCube System - License
|
||||
------------------------------------------------------------
|
||||
|
||||
The gCube/gCore software is licensed as Free Open Source software conveying to the EUPL (http://ec.europa.eu/idabc/eupl).
|
||||
The software and documentation is provided by its authors/distributors "as is" and no expressed or
|
||||
implied warranty is given for its use, quality or fitness for a particular case.
|
||||
|
|
@ -0,0 +1,2 @@
|
|||
Lucio lelii (lucio.lelii@isti.cnr.it), CNR Pisa,
|
||||
Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo".
|
||||
|
|
@ -0,0 +1,47 @@
|
|||
The gCube System - spd client library
|
||||
|
||||
------------------------------------------------------------
|
||||
|
||||
This work has been partially supported by the following European projects: DILIGENT (FP6-2003-IST-2),
|
||||
D4Science (FP7-INFRA-2007-1.2.2), D4Science-II (FP7-INFRA-2008-1.2.2), iMarine (FP7-INFRASTRUCTURES-2011-2),
|
||||
and EUBrazilOpenBio (FP7-ICT-2011-EU-Brazil).
|
||||
|
||||
|
||||
Authors
|
||||
-------
|
||||
|
||||
* Lucio Lelii (lucio.lelii@isti.cnr.it), CNR Pisa,
|
||||
Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo".
|
||||
|
||||
|
||||
Version and Release Date
|
||||
------------------------
|
||||
|
||||
v. 1.0.0 (04-05-2012)
|
||||
* First release
|
||||
|
||||
|
||||
Description
|
||||
-----------
|
||||
|
||||
|
||||
|
||||
Download information
|
||||
--------------------
|
||||
|
||||
|
||||
|
||||
Documentation
|
||||
-------------
|
||||
|
||||
Documentation is available on-line from the Projects Documentation Wiki:
|
||||
https://gcube.wiki.gcube-system.org/gcube/index.php/Biodiversity_Access
|
||||
|
||||
|
||||
Licensing
|
||||
---------
|
||||
|
||||
This software is licensed under the terms you may find in the file named "LICENSE" in this directory.
|
||||
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,22 @@
|
|||
<ReleaseNotes>
|
||||
<Changeset component="org.gcube.data-access.spd-client-library.1-0-0" date="2012-09-14">
|
||||
<Change>species products discovery client library release</Change>
|
||||
</Changeset>
|
||||
<Changeset component="org.gcube.data-access.spd-client-library.1-1-0" date="2012-10-18">
|
||||
<Change>new calls added</Change>
|
||||
</Changeset>
|
||||
<Changeset component="org.gcube.data-access.spd-plugin-framework.1-2-0" date="2012-11-30">
|
||||
<Change>a bug on the Writer has been fixed</Change>
|
||||
</Changeset><Changeset component="org.gcube.data-access.spd-plugin-framework.2-0-0" date="2013-01-17">
|
||||
<Change>model part splitted in a different library</Change>
|
||||
</Changeset>
|
||||
<Changeset component="org.gcube.data-access.spd-plugin-framework.2-2-0" date="2013-01-17">
|
||||
<Change>bug fixing</Change>
|
||||
</Changeset>
|
||||
<Changeset component="org.gcube.data-access.spd-plugin-framework.2-3-0" date="2013-07-18">
|
||||
<Change>Unfold Capability for plugin added</Change>
|
||||
</Changeset>
|
||||
<Changeset component="org.gcube.data-access.spd-plugin-framework.3-1-0" date="2017-02-01">
|
||||
<Change>gCore dependency removed</Change>
|
||||
</Changeset>
|
||||
</ReleaseNotes>
|
||||
|
|
@ -0,0 +1,42 @@
|
|||
<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>${distroDirectory}</directory>
|
||||
<outputDirectory>/</outputDirectory>
|
||||
<useDefaultExcludes>true</useDefaultExcludes>
|
||||
<includes>
|
||||
<include>README</include>
|
||||
<include>LICENSE</include>
|
||||
<include>INSTALL</include>
|
||||
<include>MAINTAINERS</include>
|
||||
<include>changelog.xml</include>
|
||||
</includes>
|
||||
<fileMode>755</fileMode>
|
||||
<filtered>true</filtered>
|
||||
</fileSet>
|
||||
</fileSets>
|
||||
<files>
|
||||
<file>
|
||||
<source>${distroDirectory}/profile.xml</source>
|
||||
<outputDirectory>/</outputDirectory>
|
||||
<filtered>true</filtered>
|
||||
</file>
|
||||
<file>
|
||||
<source>target/${build.finalName}.jar</source>
|
||||
<outputDirectory>/${artifactId}</outputDirectory>
|
||||
</file>
|
||||
<file>
|
||||
<source>${distroDirectory}/svnpath.txt</source>
|
||||
<outputDirectory>/${artifactId}</outputDirectory>
|
||||
<filtered>true</filtered>
|
||||
</file>
|
||||
</files>
|
||||
</assembly>
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
<?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>${build.finalName}.jar</File>
|
||||
</Files>
|
||||
</Software>
|
||||
</Packages>
|
||||
</Profile>
|
||||
</Resource>
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,107 @@
|
|||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
|
||||
<parent>
|
||||
<groupId>org.gcube.tools</groupId>
|
||||
<artifactId>maven-parent</artifactId>
|
||||
<version>1.0.0</version>
|
||||
</parent>
|
||||
|
||||
<groupId>org.gcube.data.spd</groupId>
|
||||
<artifactId>spd-plugin-framework</artifactId>
|
||||
<version>3.1.0-SNAPSHOT</version>
|
||||
<name>spd-plugin-framework</name>
|
||||
<description>SPD plugin framework</description>
|
||||
<dependencies>
|
||||
|
||||
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.resources</groupId>
|
||||
<artifactId>common-gcore-resources</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.data.spd</groupId>
|
||||
<artifactId>spd-model</artifactId>
|
||||
<version>[3.0.0-SNAPSHOT,4.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.execution</groupId>
|
||||
<artifactId>grs2library</artifactId>
|
||||
<version>[2.0.0-SNAPSHOT, 3.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.data.access</groupId>
|
||||
<artifactId>streams</artifactId>
|
||||
<version>[2.0.0-SNAPSHOT, 3.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
|
||||
</dependencies>
|
||||
|
||||
<properties>
|
||||
<distroDirectory>${project.basedir}/distro</distroDirectory>
|
||||
</properties>
|
||||
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<artifactId>maven-compiler-plugin</artifactId>
|
||||
<configuration>
|
||||
<source>1.6</source>
|
||||
<target>1.6</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 +1,105 @@
|
|||
package org.gcube.data.spd.plugin.fwk;
|
||||
|
||||
import java.util.Collections;
|
||||
import java.util.Set;
|
||||
import org.gcube.common.resources.gcore.ServiceEndpoint;
|
||||
import org.gcube.data.spd.model.Conditions;
|
||||
import org.gcube.data.spd.model.PropertySupport;
|
||||
import org.gcube.data.spd.model.RepositoryInfo;
|
||||
import org.gcube.data.spd.model.products.ResultItem;
|
||||
import org.gcube.data.spd.model.util.Capabilities;
|
||||
import org.gcube.data.spd.plugin.fwk.capabilities.ClassificationCapability;
|
||||
import org.gcube.data.spd.plugin.fwk.capabilities.ExpansionCapability;
|
||||
import org.gcube.data.spd.plugin.fwk.capabilities.MappingCapability;
|
||||
import org.gcube.data.spd.plugin.fwk.capabilities.OccurrencesCapability;
|
||||
import org.gcube.data.spd.plugin.fwk.capabilities.UnfoldCapability;
|
||||
|
||||
public abstract class AbstractPlugin implements PropertySupport, Searchable<ResultItem>{
|
||||
|
||||
private boolean initialized = false;
|
||||
|
||||
private boolean useCache= false;
|
||||
|
||||
public void initialize(ServiceEndpoint resource) throws Exception{
|
||||
initialized= true;
|
||||
}
|
||||
|
||||
public void update(ServiceEndpoint resource) throws Exception{}
|
||||
|
||||
public void shutdown() throws Exception{}
|
||||
|
||||
public ClassificationCapability getClassificationInterface(){return null;};
|
||||
|
||||
public MappingCapability getMappingInterface(){return null;};
|
||||
|
||||
public ExpansionCapability getExpansionInterface(){return null;};
|
||||
|
||||
public OccurrencesCapability getOccurrencesInterface(){return null;};
|
||||
|
||||
public UnfoldCapability getUnfoldInterface(){return null;};
|
||||
|
||||
public Set<Conditions> getSupportedProperties(){
|
||||
return Collections.emptySet();
|
||||
}
|
||||
|
||||
public Set<Capabilities> getSupportedCapabilities() {
|
||||
return Collections.emptySet();
|
||||
}
|
||||
|
||||
public abstract RepositoryInfo getRepositoryInfo();
|
||||
|
||||
@Override
|
||||
public Class<ResultItem> getHandledClass() {
|
||||
return ResultItem.class;
|
||||
}
|
||||
|
||||
/*
|
||||
@Override
|
||||
public abstract void searchByScientificName(String word,
|
||||
ObjectWriter<ResultItem> writer, Condition... properties) throws ExternalRepositoryException;
|
||||
*/
|
||||
public abstract String getRepositoryName();
|
||||
|
||||
public abstract String getDescription();
|
||||
|
||||
|
||||
public boolean isUseCache() {
|
||||
return useCache;
|
||||
}
|
||||
|
||||
public void setUseCache(boolean useCache) {
|
||||
this.useCache = useCache;
|
||||
}
|
||||
|
||||
public boolean isInitialized() {
|
||||
return initialized;
|
||||
}
|
||||
|
||||
public boolean isRemote(){
|
||||
return false;
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return getRepositoryName()+"(use-cache="+isUseCache()+")";
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean equals(Object obj) {
|
||||
if (obj==null) return false;
|
||||
AbstractPlugin ap = (AbstractPlugin) obj;
|
||||
if (ap.getRepositoryName()==null || ap.getRepositoryName().equals("")) return false;
|
||||
return ap.getRepositoryName().equals(this.getRepositoryName());
|
||||
}
|
||||
|
||||
@Override
|
||||
public int hashCode() {
|
||||
return this.getRepositoryName().hashCode();
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
package org.gcube.data.spd.plugin.fwk;
|
||||
|
||||
public class Labels {
|
||||
|
||||
public static final String RANK_LABEL="rank";
|
||||
public static final String ACCORDINGTO_LABEL="accordingTo";
|
||||
public static final String SCIENTIFICNAME_LABEL="scientificName";
|
||||
public static final String COMMONNAME_LABEL="commonName";
|
||||
public static final String COMMONNAMES_LABEL="commonNames";
|
||||
public static final String PROVIDER_LABEL="provider";
|
||||
public static final String CITATION_LABEL="citation";
|
||||
public static final String PARENT_TAG="parent";
|
||||
|
||||
public static final String PRODUCTS_LABEL="products";
|
||||
|
||||
public static final String PRODUCT_LABEL="product";
|
||||
|
||||
public static final String TYPE_LABEL="type";
|
||||
public static final String KEY_LABEL="key";
|
||||
|
||||
public static final String DATASET_TAG="dataSet";
|
||||
public static final String DATAPROVIDER_TAG="dataProvider";
|
||||
public static final String NAME_TAG = "name";
|
||||
public static final String LANGUAGE_TAG = "language";
|
||||
public static final String COUNT_LABEL = "count";
|
||||
|
||||
public static final String CREDITS_LABEL = "credits";
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,15 @@
|
|||
package org.gcube.data.spd.plugin.fwk;
|
||||
|
||||
import org.gcube.data.spd.model.Condition;
|
||||
import org.gcube.data.spd.model.exceptions.ExternalRepositoryException;
|
||||
import org.gcube.data.spd.model.products.ResultElement;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ObjectWriter;
|
||||
|
||||
|
||||
|
||||
public interface Searchable<T extends ResultElement>{
|
||||
|
||||
public void searchByScientificName(String word, ObjectWriter<T> writer, Condition ... properties) throws ExternalRepositoryException;
|
||||
|
||||
public Class<T> getHandledClass();
|
||||
}
|
||||
|
|
@ -0,0 +1,60 @@
|
|||
package org.gcube.data.spd.plugin.fwk.capabilities;
|
||||
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.data.spd.model.PropertySupport;
|
||||
import org.gcube.data.spd.model.exceptions.ExternalRepositoryException;
|
||||
import org.gcube.data.spd.model.exceptions.IdNotValidException;
|
||||
import org.gcube.data.spd.model.exceptions.MethodNotSupportedException;
|
||||
import org.gcube.data.spd.model.products.TaxonomyItem;
|
||||
import org.gcube.data.spd.plugin.fwk.Searchable;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ClosableWriter;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ObjectWriter;
|
||||
|
||||
|
||||
public abstract class ClassificationCapability implements PropertySupport, Searchable<TaxonomyItem>{
|
||||
|
||||
/**
|
||||
* retrieves all children giving a taxon id
|
||||
*
|
||||
* @param taxonId the taxon id
|
||||
* @return a list of taxon
|
||||
*/
|
||||
public abstract List<TaxonomyItem> retrieveTaxonChildrenByTaxonId(String taxonId) throws IdNotValidException, ExternalRepositoryException;
|
||||
|
||||
|
||||
/**
|
||||
* retrieves taxon by ids
|
||||
*
|
||||
* @param ids the taxon ids
|
||||
* @return a taxon
|
||||
*/
|
||||
public abstract void retrieveTaxonByIds(Iterator<String> ids, ClosableWriter<TaxonomyItem> writer) throws ExternalRepositoryException;
|
||||
|
||||
/**
|
||||
* retrieves taxon by id
|
||||
*
|
||||
* @param taxonId the taxon id
|
||||
* @return a taxon
|
||||
*/
|
||||
public abstract TaxonomyItem retrieveTaxonById(String id) throws IdNotValidException, ExternalRepositoryException;
|
||||
|
||||
/**
|
||||
*
|
||||
* retrieve a list of synonyms
|
||||
*
|
||||
* @param writer
|
||||
* @param ids
|
||||
*/
|
||||
public void getSynonymnsById(ObjectWriter<TaxonomyItem> writer, String id) throws IdNotValidException, MethodNotSupportedException, ExternalRepositoryException{
|
||||
throw new MethodNotSupportedException();
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public Class<TaxonomyItem> getHandledClass() {
|
||||
return TaxonomyItem.class;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
package org.gcube.data.spd.plugin.fwk.capabilities;
|
||||
|
||||
import org.gcube.data.spd.model.exceptions.ExternalRepositoryException;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ObjectWriter;
|
||||
|
||||
public interface ExpansionCapability {
|
||||
|
||||
public void getSynonyms(ObjectWriter<String> writer, String scientifcName ) throws ExternalRepositoryException;
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,11 @@
|
|||
package org.gcube.data.spd.plugin.fwk.capabilities;
|
||||
|
||||
|
||||
import org.gcube.data.spd.model.products.Image;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ObjectWriter;
|
||||
|
||||
public interface ImagesCapability {
|
||||
|
||||
public void getImagesById(ObjectWriter<Image> writer, String ... ids) throws Exception;
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,17 @@
|
|||
package org.gcube.data.spd.plugin.fwk.capabilities;
|
||||
|
||||
import org.gcube.data.spd.model.exceptions.ExternalRepositoryException;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ObjectWriter;
|
||||
|
||||
public interface MappingCapability{
|
||||
|
||||
/**
|
||||
*
|
||||
* this method returns a set of scientific names related to the common name passed as input
|
||||
*
|
||||
* @param commonName to Map
|
||||
* @return a set of scientificNames
|
||||
* @throws Exception
|
||||
*/
|
||||
public void getRelatedScientificNames(ObjectWriter<String> writer, String commonName) throws ExternalRepositoryException;
|
||||
}
|
||||
|
|
@ -0,0 +1,38 @@
|
|||
package org.gcube.data.spd.plugin.fwk.capabilities;
|
||||
|
||||
import java.util.Iterator;
|
||||
|
||||
import org.gcube.data.spd.model.PropertySupport;
|
||||
import org.gcube.data.spd.model.exceptions.ExternalRepositoryException;
|
||||
import org.gcube.data.spd.model.products.OccurrencePoint;
|
||||
import org.gcube.data.spd.plugin.fwk.Searchable;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ClosableWriter;
|
||||
|
||||
public abstract class OccurrencesCapability implements PropertySupport, Searchable<OccurrencePoint>{
|
||||
|
||||
/**
|
||||
* retrieves all occurrences for the given ids
|
||||
*
|
||||
* @param writer the stream where the elements must be wrote
|
||||
* @param keys a list of products keys
|
||||
* @throws Exception
|
||||
*/
|
||||
public abstract void getOccurrencesByProductKeys(ClosableWriter<OccurrencePoint> writer, Iterator<String> keys) throws ExternalRepositoryException;
|
||||
|
||||
/**
|
||||
* retrieves all occurrences for the given ids
|
||||
*
|
||||
* @param writer the stream where the elements must be wrote
|
||||
* @param ids a list of occurrence ids
|
||||
* @throws Exception
|
||||
*/
|
||||
public abstract void getOccurrencesByIds(ClosableWriter<OccurrencePoint> writer, Iterator<String> ids) throws ExternalRepositoryException;
|
||||
|
||||
@Override
|
||||
public Class<OccurrencePoint> getHandledClass() {
|
||||
return OccurrencePoint.class;
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
package org.gcube.data.spd.plugin.fwk.capabilities;
|
||||
|
||||
import org.gcube.data.spd.model.exceptions.ExternalRepositoryException;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.ObjectWriter;
|
||||
|
||||
public interface UnfoldCapability {
|
||||
|
||||
public void unfold(ObjectWriter<String> writer, String scientificName) throws ExternalRepositoryException;
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
package org.gcube.data.spd.plugin.fwk.readers;
|
||||
|
||||
import java.util.concurrent.BlockingQueue;
|
||||
|
||||
import org.gcube.data.spd.plugin.fwk.writers.rswrapper.AbstractLocalWrapper;
|
||||
import org.gcube.data.streams.Stream;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
|
||||
public abstract class AbstractLocalReader<T> implements Stream<T>{
|
||||
|
||||
protected static final Logger logger = LoggerFactory.getLogger(AbstractLocalReader.class);
|
||||
|
||||
protected BlockingQueue<T> queue;
|
||||
|
||||
protected T element = null;
|
||||
|
||||
protected int timeoutInSeconds= 2;
|
||||
|
||||
AbstractLocalWrapper<T> wrapper ;
|
||||
|
||||
public AbstractLocalReader(AbstractLocalWrapper<T> wrapper) {
|
||||
queue = wrapper.getQueue();
|
||||
this.wrapper = wrapper;
|
||||
}
|
||||
|
||||
|
||||
|
||||
public void setTimeoutInSeconds(int timeoutInSeconds) {
|
||||
this.timeoutInSeconds = timeoutInSeconds;
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
public T next() {
|
||||
return element;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void remove() {}
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
package org.gcube.data.spd.plugin.fwk.readers;
|
||||
|
||||
import java.net.URI;
|
||||
import java.util.concurrent.TimeUnit;
|
||||
|
||||
import org.gcube.data.spd.plugin.fwk.writers.rswrapper.AbstractLocalWrapper;
|
||||
|
||||
public class LocalReader<T> extends AbstractLocalReader<T> {
|
||||
|
||||
public LocalReader(AbstractLocalWrapper<T> wrapper) {
|
||||
super(wrapper);
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean hasNext() {
|
||||
if (queue==null) return false;
|
||||
else{
|
||||
try {
|
||||
element=null;
|
||||
while (!this.wrapper.isClosed() && element==null )
|
||||
element= queue.poll(timeoutInSeconds, TimeUnit.SECONDS);
|
||||
if (element ==null) element=queue.poll();
|
||||
} catch (InterruptedException e) {
|
||||
logger.warn("the queue is empty",e);
|
||||
}
|
||||
return element!=null;
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public URI locator() {
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void close() {
|
||||
logger.debug("closing reader");
|
||||
if (wrapper.isClosed())
|
||||
wrapper.disposeBuffer();
|
||||
else wrapper.close();
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean isClosed() {
|
||||
return wrapper.isClosed();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
package org.gcube.data.spd.plugin.fwk.readers;
|
||||
|
||||
import org.gcube.data.spd.model.binding.Bindings;
|
||||
import org.gcube.data.spd.model.products.OccurrencePoint;
|
||||
|
||||
|
||||
|
||||
public class OccurrencesReader extends RSReader<OccurrencePoint>{
|
||||
|
||||
public OccurrencesReader(String locator) throws Exception {
|
||||
super(locator);
|
||||
}
|
||||
|
||||
@Override
|
||||
public OccurrencePoint transform(String serializedItem) throws Exception {
|
||||
return Bindings.fromXml(serializedItem);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,51 @@
|
|||
package org.gcube.data.spd.plugin.fwk.readers;
|
||||
|
||||
import gr.uoa.di.madgik.grs.reader.ForwardReader;
|
||||
import gr.uoa.di.madgik.grs.reader.GRS2ReaderException;
|
||||
import gr.uoa.di.madgik.grs.record.GenericRecord;
|
||||
import gr.uoa.di.madgik.grs.record.field.StringField;
|
||||
import java.net.URI;
|
||||
import java.util.Iterator;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public abstract class RSReader<T> implements Iterator<T>{
|
||||
|
||||
private static final Logger logger = LoggerFactory.getLogger(RSReader.class);
|
||||
private Iterator<GenericRecord> it;
|
||||
private ForwardReader<GenericRecord> reader;
|
||||
|
||||
public RSReader(String locator) throws Exception{
|
||||
reader=new ForwardReader<GenericRecord>(new URI(locator));
|
||||
reader.setIteratorTimeout(3000);
|
||||
it =reader.iterator();
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean hasNext() {
|
||||
if (it.hasNext()) return true;
|
||||
else {
|
||||
try {
|
||||
reader.close();
|
||||
} catch (GRS2ReaderException e) {
|
||||
logger.error("error closing reader",e);
|
||||
}
|
||||
return false;
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public T next() {
|
||||
try {
|
||||
return transform(((StringField)it.next().getField("result")).getPayload());
|
||||
} catch (Exception e) {
|
||||
logger.error("error getting tree",e);
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
public abstract T transform(String serializedItem) throws Exception;
|
||||
|
||||
@Override
|
||||
public void remove() {}
|
||||
}
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
package org.gcube.data.spd.plugin.fwk.readers;
|
||||
|
||||
import org.gcube.data.spd.model.binding.Bindings;
|
||||
import org.gcube.data.spd.model.products.ResultItem;
|
||||
|
||||
|
||||
|
||||
public class ResultItemReader extends RSReader<ResultItem>{
|
||||
|
||||
public ResultItemReader(String locator) throws Exception {
|
||||
super(locator);
|
||||
}
|
||||
|
||||
@Override
|
||||
public ResultItem transform(String serializedItem) throws Exception {
|
||||
return Bindings.fromXml(serializedItem);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,16 @@
|
|||
package org.gcube.data.spd.plugin.fwk.readers;
|
||||
|
||||
public class StringReader extends RSReader<String>{
|
||||
|
||||
public StringReader(String locator) throws Exception {
|
||||
super(locator);
|
||||
}
|
||||
|
||||
@Override
|
||||
public String transform(String serializedItem) throws Exception {
|
||||
return serializedItem;
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
package org.gcube.data.spd.plugin.fwk.util;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
import javax.xml.bind.annotation.XmlAccessType;
|
||||
import javax.xml.bind.annotation.XmlAccessorType;
|
||||
import javax.xml.bind.annotation.XmlAttribute;
|
||||
import javax.xml.bind.annotation.XmlRootElement;
|
||||
|
||||
|
||||
@XmlRootElement
|
||||
@XmlAccessorType(XmlAccessType.NONE)
|
||||
public class ElementProperty implements Serializable{
|
||||
|
||||
|
||||
|
||||
/**
|
||||
*
|
||||
*/
|
||||
private static final long serialVersionUID = 1L;
|
||||
|
||||
|
||||
@XmlAttribute
|
||||
private String name;
|
||||
@XmlAttribute
|
||||
private String value;
|
||||
|
||||
protected ElementProperty() {
|
||||
super();
|
||||
}
|
||||
|
||||
public ElementProperty(String name, String value) {
|
||||
super();
|
||||
this.name = name;
|
||||
this.value = value;
|
||||
}
|
||||
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
|
||||
public String getValue() {
|
||||
return value;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,122 @@
|
|||
package org.gcube.data.spd.plugin.fwk.util;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileWriter;
|
||||
import java.io.IOException;
|
||||
import java.text.DateFormat;
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.Calendar;
|
||||
|
||||
import javax.xml.bind.JAXBException;
|
||||
|
||||
import org.gcube.data.spd.model.binding.Bindings;
|
||||
import org.gcube.data.spd.model.exceptions.IdNotValidException;
|
||||
import org.gcube.data.spd.model.products.OccurrencePoint;
|
||||
import org.gcube.data.spd.model.products.ResultElement;
|
||||
import org.gcube.data.spd.plugin.fwk.readers.OccurrencesReader;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public class Util {
|
||||
|
||||
private static final Logger logger = LoggerFactory.getLogger(Util.class);
|
||||
|
||||
public static String keyEnrichment(String provider, String key){
|
||||
return provider+":"+key;
|
||||
}
|
||||
|
||||
public static String getProviderFromKey(String key) throws IdNotValidException{
|
||||
int index = key.indexOf(":");
|
||||
if (index==-1) throw new IdNotValidException();
|
||||
return key.substring(0, index);
|
||||
}
|
||||
|
||||
public static String getIdFromKey(String key) throws IdNotValidException {
|
||||
int index = key.indexOf(":");
|
||||
if (index==-1) throw new IdNotValidException();
|
||||
return key.substring(index+1, key.length());
|
||||
}
|
||||
|
||||
public static <T extends ResultElement> T copy(T obj) throws JAXBException {
|
||||
return Bindings.<T>fromXml(Bindings.<T>toXml(obj));
|
||||
}
|
||||
|
||||
public static File getDarwinCoreFile(OccurrencesReader reader) throws Exception{
|
||||
|
||||
DateFormat df = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss");
|
||||
|
||||
FileWriter writer = null;
|
||||
|
||||
|
||||
try{
|
||||
File returnFile = File.createTempFile("darwinCore", "xml");
|
||||
writer = new FileWriter(returnFile);
|
||||
|
||||
|
||||
writer.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
|
||||
writer.append("<SimpleDarwinRecordSet xmlns=\"http://rs.tdwg.org/dwc/xsd/simpledarwincore/\" xmlns:dc=\"http://purl.org/dc/terms/\" xmlns:dwc=\"http://rs.tdwg.org/dwc/terms/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://rs.tdwg.org/dwc/xsd/simpledarwincore/ http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd\">");
|
||||
|
||||
while (reader.hasNext()){
|
||||
|
||||
writer.append("<SimpleDarwinRecord>");
|
||||
writer.append("<dc:language>en</dc:language>");
|
||||
|
||||
OccurrencePoint occurrence= reader.next();
|
||||
|
||||
if (occurrence.getModified() != null)
|
||||
writer.append("<dc:modified>" + df.format(occurrence.getModified().getTime()) + "</dc:modified>");
|
||||
if (occurrence.getBasisOfRecord() != null)
|
||||
writer.append("<dwc:basisOfRecord>" + occurrence.getBasisOfRecord().name() + "</dwc:basisOfRecord>");
|
||||
if (occurrence.getInstitutionCode() != null)
|
||||
writer.append("<dwc:institutionCode>" + occurrence.getInstitutionCode() + "</dwc:institutionCode>");
|
||||
if (occurrence.getCollectionCode() != null)
|
||||
writer.append("<dwc:collectionCode>" + occurrence.getCollectionCode() + "</dwc:collectionCode>");
|
||||
if (occurrence.getCatalogueNumber() != null)
|
||||
writer.append("<dwc:catalogNumber>" + occurrence.getCatalogueNumber() + "</dwc:catalogNumber>");
|
||||
if (occurrence.getRecordedBy() != null)
|
||||
writer.append("<dwc:recordedBy>" + occurrence.getRecordedBy() + "</dwc:recordedBy>");
|
||||
if (occurrence.getScientificName() != null)
|
||||
writer.append("<dwc:scientificName>" + occurrence.getScientificName() + "</dwc:scientificName>");
|
||||
if (occurrence.getKingdom() != null)
|
||||
writer.append("<dwc:kingdom>" + occurrence.getKingdom() + "</dwc:kingdom>");
|
||||
if (occurrence.getFamily() != null)
|
||||
writer.append("<dwc:family>" + occurrence.getFamily() + "</dwc:family>");
|
||||
if (occurrence.getLocality() != null)
|
||||
writer.append("<dwc:locality>" + occurrence.getLocality() + "</dwc:locality>");
|
||||
if (occurrence.getEventDate() != null)
|
||||
{
|
||||
writer.append("<dwc:eventDate>" + df.format(occurrence.getEventDate().getTime()) + "</dwc:eventDate>");
|
||||
writer.append("<dwc:year>" + occurrence.getEventDate().get(Calendar.YEAR) + "</dwc:year>");
|
||||
}
|
||||
if (occurrence.getDecimalLatitude() != 0.0)
|
||||
writer.append("<dwc:decimalLatitude>" + occurrence.getDecimalLatitude() + "</dwc:decimalLatitude>");
|
||||
if (occurrence.getDecimalLongitude() != 0.0)
|
||||
writer.append("<dwc:decimalLongitude>" + occurrence.getDecimalLongitude() + "</dwc:decimalLongitude>");
|
||||
if (occurrence.getCoordinateUncertaintyInMeters() != null)
|
||||
writer.append("<dwc:coordinateUncertaintyInMeters>" + occurrence.getCoordinateUncertaintyInMeters() + "</dwc:coordinateUncertaintyInMeters>");
|
||||
if (occurrence.getMaxDepth() != 0.0)
|
||||
writer.append("<dwc:maximumDepthInMeters>" + occurrence.getMaxDepth() + "</dwc:maximumDepthInMeters>");
|
||||
if (occurrence.getMinDepth() != 0.0)
|
||||
writer.append("<dwc:minimumDepthInMeters>" + occurrence.getMinDepth() + "</dwc:minimumDepthInMeters>");
|
||||
|
||||
writer.append("</SimpleDarwinRecord>");
|
||||
}
|
||||
|
||||
writer.append("</SimpleDarwinRecordSet>");
|
||||
writer.flush();
|
||||
writer.close();
|
||||
return returnFile;
|
||||
}catch (Exception e) {
|
||||
logger.error("error writeing occurrences as darwin core",e);
|
||||
throw e;
|
||||
}finally{
|
||||
try {
|
||||
writer.close();
|
||||
} catch (IOException e) {
|
||||
logger.warn("error closing the output stream",e);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
package org.gcube.data.spd.plugin.fwk.writers;
|
||||
|
||||
import org.gcube.data.spd.plugin.fwk.writers.rswrapper.AbstractWrapper;
|
||||
|
||||
|
||||
|
||||
public abstract class AbstractWriter<T> implements ClosableWriter<T>{
|
||||
|
||||
//private Logger logger= LoggerFactory.getLogger(AbstractWriter.class);
|
||||
|
||||
protected boolean closed;
|
||||
|
||||
private int links =0;
|
||||
|
||||
private AbstractWrapper<T> wrapper;
|
||||
|
||||
protected int wrote;
|
||||
|
||||
protected AbstractWriter(AbstractWrapper<T> wrapper) {
|
||||
this.wrapper = wrapper;
|
||||
this.wrapper.register();
|
||||
}
|
||||
|
||||
protected AbstractWrapper<T> getWrapper() {
|
||||
return wrapper;
|
||||
}
|
||||
|
||||
public synchronized void register(){
|
||||
links++;
|
||||
}
|
||||
|
||||
public synchronized void register(int links){
|
||||
this.links+=links;
|
||||
}
|
||||
|
||||
public synchronized void close() {
|
||||
links--;
|
||||
if (links<=0){
|
||||
if (!closed){
|
||||
if (!this.wrapper.isClosed())this.wrapper.unregister();
|
||||
closed=true;
|
||||
} else throw new IllegalStateException("writer already closed");
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,8 @@
|
|||
package org.gcube.data.spd.plugin.fwk.writers;
|
||||
|
||||
|
||||
public interface ClosableWriter<T> extends ObjectWriter<T> {
|
||||
|
||||
|
||||
public void close();
|
||||
}
|
||||
|
|
@ -0,0 +1,17 @@
|
|||
package org.gcube.data.spd.plugin.fwk.writers;
|
||||
|
||||
import org.gcube.data.spd.model.exceptions.StreamException;
|
||||
|
||||
|
||||
|
||||
|
||||
public interface ObjectWriter<T> {
|
||||
|
||||
public boolean write(T t);
|
||||
|
||||
public boolean write(StreamException error);
|
||||
|
||||
public boolean isAlive();
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,13 @@
|
|||
package org.gcube.data.spd.plugin.fwk.writers;
|
||||
|
||||
public interface RecordWriter<T> {
|
||||
|
||||
boolean put(T element);
|
||||
|
||||
boolean put(Exception error);
|
||||
|
||||
void close();
|
||||
|
||||
boolean isClosed();
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,32 @@
|
|||
package org.gcube.data.spd.plugin.fwk.writers;
|
||||
|
||||
import org.gcube.data.spd.model.products.ResultElement;
|
||||
import org.gcube.data.spd.plugin.fwk.util.Util;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public abstract class ResultElementWriterManager<T extends ResultElement> extends WriterManager<T> {
|
||||
|
||||
private static final Logger logger = LoggerFactory.getLogger(ResultElementWriterManager.class);
|
||||
|
||||
protected String provider;
|
||||
|
||||
public ResultElementWriterManager(String provider) {
|
||||
super();
|
||||
this.provider = provider;
|
||||
}
|
||||
|
||||
@Override
|
||||
public T enrich(T obj) {
|
||||
try{
|
||||
return _enrich(Util.<T>copy(obj));
|
||||
}catch (Exception e) {
|
||||
logger.error("error enriching object",e);
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
protected abstract T _enrich(T obj);
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,79 @@
|
|||
package org.gcube.data.spd.plugin.fwk.writers;
|
||||
|
||||
|
||||
|
||||
import org.gcube.data.spd.model.exceptions.InvalidRecordException;
|
||||
import org.gcube.data.spd.model.exceptions.StreamBlockingException;
|
||||
import org.gcube.data.spd.model.exceptions.StreamException;
|
||||
import org.gcube.data.spd.model.exceptions.WrapperAlreadyDisposedException;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.rswrapper.AbstractWrapper;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
|
||||
public class Writer<F> extends AbstractWriter<F>{
|
||||
|
||||
private static final Logger logger = LoggerFactory.getLogger(Writer.class);
|
||||
|
||||
private WriterManager<F> manager = new DefaultWriter();
|
||||
|
||||
|
||||
public Writer(AbstractWrapper<F> wrapper) {
|
||||
super(wrapper);
|
||||
}
|
||||
|
||||
public Writer(AbstractWrapper<F> wrapper, WriterManager<F> manager) {
|
||||
super(wrapper);
|
||||
this.manager = manager;
|
||||
}
|
||||
|
||||
public class DefaultWriter extends WriterManager<F>{}
|
||||
|
||||
|
||||
@Override
|
||||
public synchronized boolean write(F t) {
|
||||
if(this.getWrapper().isClosed()) return false;
|
||||
if (manager.filter(t)){
|
||||
try{
|
||||
getWrapper().add(manager.enrich(t));
|
||||
}catch (InvalidRecordException e) {
|
||||
logger.warn("error putting a result in the Writer",e);
|
||||
return false;
|
||||
}catch (WrapperAlreadyDisposedException e) {
|
||||
logger.warn("wrapper already disposed",e);
|
||||
return false;
|
||||
}
|
||||
} else{
|
||||
logger.debug("a result has been filtered");
|
||||
return false;
|
||||
}
|
||||
wrote++;
|
||||
return true;
|
||||
}
|
||||
|
||||
@Override
|
||||
public synchronized boolean write(StreamException error) {
|
||||
try{
|
||||
getWrapper().add(error);
|
||||
}catch (InvalidRecordException e) {
|
||||
logger.warn("error putting execption in the Writer",e);
|
||||
return false;
|
||||
}catch (WrapperAlreadyDisposedException e) {
|
||||
logger.warn("wrapper already disposed",e);
|
||||
return false;
|
||||
}
|
||||
if (error instanceof StreamBlockingException ){
|
||||
getWrapper().close();
|
||||
return false;
|
||||
}
|
||||
return true;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean isAlive() {
|
||||
return !getWrapper().isClosed();
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
package org.gcube.data.spd.plugin.fwk.writers;
|
||||
|
||||
import org.gcube.data.streams.exceptions.StreamSkipSignal;
|
||||
import org.gcube.data.streams.generators.Generator;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public abstract class WriterManager<T> implements Generator<T, T> {
|
||||
|
||||
private static final Logger logger = LoggerFactory.getLogger(WriterManager.class);
|
||||
|
||||
public T enrich(T obj){ return obj;}
|
||||
|
||||
public boolean filter(T obj){return true;}
|
||||
|
||||
@Override
|
||||
public T yield(T element) {
|
||||
try {
|
||||
T enrichedElement = this.enrich(element);
|
||||
if (enrichedElement==null) throw new Exception("error enriching element");
|
||||
return enrichedElement;
|
||||
} catch (Exception e) {
|
||||
logger.debug("skipping the result", e);
|
||||
throw new StreamSkipSignal();
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,36 @@
|
|||
package org.gcube.data.spd.plugin.fwk.writers.rswrapper;
|
||||
|
||||
import java.util.UUID;
|
||||
import java.util.concurrent.BlockingQueue;
|
||||
|
||||
|
||||
public abstract class AbstractLocalWrapper<T> extends AbstractWrapper<T> {
|
||||
|
||||
private String locator;
|
||||
protected boolean closed = false;
|
||||
|
||||
public AbstractLocalWrapper() {
|
||||
super();
|
||||
this.locator = UUID.randomUUID().toString();
|
||||
}
|
||||
|
||||
public AbstractLocalWrapper(int queueSize) {
|
||||
super();
|
||||
this.locator = UUID.randomUUID().toString();
|
||||
}
|
||||
|
||||
public abstract BlockingQueue<T> getQueue();
|
||||
|
||||
@Override
|
||||
public String getLocator() {
|
||||
return this.locator;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean isClosed() {
|
||||
return closed;
|
||||
}
|
||||
|
||||
public abstract void disposeBuffer();
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,42 @@
|
|||
package org.gcube.data.spd.plugin.fwk.writers.rswrapper;
|
||||
|
||||
import org.gcube.data.spd.model.exceptions.InvalidRecordException;
|
||||
import org.gcube.data.spd.model.exceptions.StreamException;
|
||||
import org.gcube.data.spd.model.exceptions.WrapperAlreadyDisposedException;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public abstract class AbstractWrapper<T> {
|
||||
|
||||
Logger logger= LoggerFactory.getLogger(AbstractWrapper.class);
|
||||
|
||||
protected int links;
|
||||
|
||||
public abstract String getLocator();
|
||||
|
||||
public abstract boolean add(T result) throws InvalidRecordException, WrapperAlreadyDisposedException;
|
||||
|
||||
public abstract boolean add(StreamException result) throws InvalidRecordException, WrapperAlreadyDisposedException;
|
||||
|
||||
public abstract void close();
|
||||
|
||||
public synchronized void unregister(){
|
||||
logger.info(Thread.currentThread().getId()+" - closing wrapper");
|
||||
links--;
|
||||
if (links<=0){
|
||||
if (!this.isClosed()){
|
||||
this.close();
|
||||
}
|
||||
else throw new IllegalStateException("wrapper already closed");
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
public synchronized void register(){
|
||||
this.links++;
|
||||
}
|
||||
|
||||
public abstract boolean isClosed();
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,118 @@
|
|||
package org.gcube.data.spd.plugin.fwk.writers.rswrapper;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.UUID;
|
||||
import java.util.concurrent.ArrayBlockingQueue;
|
||||
import java.util.concurrent.TimeUnit;
|
||||
|
||||
import org.gcube.data.spd.model.exceptions.InvalidRecordException;
|
||||
import org.gcube.data.spd.model.exceptions.StreamException;
|
||||
import org.gcube.data.spd.model.exceptions.WrapperAlreadyDisposedException;
|
||||
|
||||
import java.util.Collections;
|
||||
|
||||
|
||||
public class LocalWrapper<T> extends AbstractLocalWrapper<T> {
|
||||
|
||||
private static Map<String, LocalWrapper<?>> wrapperLocatorMap = new HashMap<String, LocalWrapper<?>>();
|
||||
|
||||
public static LocalWrapper<?> getWrapper(String locator){
|
||||
return wrapperLocatorMap.get(locator);
|
||||
}
|
||||
|
||||
private String locator;
|
||||
|
||||
private ArrayBlockingQueue<T> queue;
|
||||
|
||||
private List<StreamException> errorList = new ArrayList<StreamException>();
|
||||
|
||||
private boolean forceOpen = false;
|
||||
|
||||
private int timeoutTimeInMinutes =1;
|
||||
|
||||
public LocalWrapper() {
|
||||
super();
|
||||
this.locator = UUID.randomUUID().toString();
|
||||
this.queue = new ArrayBlockingQueue<T>(100);
|
||||
}
|
||||
|
||||
public LocalWrapper(int queueSize) {
|
||||
super();
|
||||
this.locator = UUID.randomUUID().toString();
|
||||
this.queue = new ArrayBlockingQueue<T>(queueSize);
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public String getLocator() {
|
||||
return this.locator;
|
||||
}
|
||||
|
||||
@Override
|
||||
public synchronized boolean add(T input) throws InvalidRecordException, WrapperAlreadyDisposedException {
|
||||
if (this.closed) new WrapperAlreadyDisposedException("the local wrapper has been disposed");
|
||||
try{
|
||||
return this.queue.offer(input, timeoutTimeInMinutes,TimeUnit.MINUTES);
|
||||
}catch (InterruptedException e) {
|
||||
this.close();
|
||||
this.queue= null;
|
||||
throw new WrapperAlreadyDisposedException("the local wrapper has been disposed");
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void close(){
|
||||
if (!isForceOpen()){
|
||||
this.closed= true;
|
||||
}
|
||||
else logger.warn("cannot close the Wrapper, forceOpen enabled");
|
||||
}
|
||||
|
||||
@Override
|
||||
public ArrayBlockingQueue<T> getQueue(){
|
||||
return queue;
|
||||
}
|
||||
|
||||
|
||||
|
||||
public void setTimeoutTimeInMinutes(int timeoutTimeInMinutes) {
|
||||
this.timeoutTimeInMinutes = timeoutTimeInMinutes;
|
||||
}
|
||||
|
||||
|
||||
public boolean isForceOpen() {
|
||||
return forceOpen;
|
||||
}
|
||||
|
||||
public void forceOpen() {
|
||||
this.forceOpen = true;
|
||||
}
|
||||
|
||||
public void disableForceOpen() {
|
||||
this.forceOpen = false;
|
||||
}
|
||||
|
||||
public void disableForceOpenAndClose() {
|
||||
this.forceOpen = false;
|
||||
this.close();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void disposeBuffer() {
|
||||
queue = null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean add(StreamException result) throws InvalidRecordException,
|
||||
WrapperAlreadyDisposedException {
|
||||
errorList.add(result);
|
||||
return true;
|
||||
}
|
||||
|
||||
public List<StreamException> getErrors(){
|
||||
return Collections.unmodifiableList(this.errorList);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,75 @@
|
|||
package org.gcube.data.spd.plugin.fwk.writers.rswrapper;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
import java.util.UUID;
|
||||
|
||||
import org.gcube.data.spd.model.exceptions.InvalidRecordException;
|
||||
import org.gcube.data.spd.model.exceptions.StreamException;
|
||||
import org.gcube.data.spd.model.exceptions.WrapperAlreadyDisposedException;
|
||||
import org.gcube.data.spd.plugin.fwk.writers.RecordWriter;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
|
||||
public class ResultWrapper<T> extends AbstractWrapper<T>{
|
||||
|
||||
|
||||
private static final Logger logger = LoggerFactory.getLogger(ResultWrapper.class);
|
||||
|
||||
private static Map<String, ResultWrapper<?>> wrapperLocatorMap = new HashMap<String, ResultWrapper<?>>();
|
||||
|
||||
public static ResultWrapper<?> getWrapper(String locator){
|
||||
return wrapperLocatorMap.get(locator);
|
||||
}
|
||||
|
||||
private String locator;
|
||||
|
||||
private RecordWriter<T> writer=null;
|
||||
|
||||
|
||||
public ResultWrapper(RecordWriter<T> rw) {
|
||||
this.writer = rw;
|
||||
this.locator = UUID.randomUUID().toString();
|
||||
}
|
||||
|
||||
|
||||
|
||||
public synchronized boolean add(T input) throws InvalidRecordException, WrapperAlreadyDisposedException{
|
||||
|
||||
try {
|
||||
return writer.put(input);
|
||||
}catch (Exception e) {
|
||||
logger.trace("the writer is already disposed (trying to write something when it is closed)");
|
||||
throw new WrapperAlreadyDisposedException(e);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
public void close(){
|
||||
this.writer.close();
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public boolean isClosed() {
|
||||
return this.writer.isClosed();
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean add(StreamException result) throws InvalidRecordException,
|
||||
WrapperAlreadyDisposedException {
|
||||
try {
|
||||
return writer.put(result);
|
||||
}catch (Exception e) {
|
||||
logger.trace("the writer is already disposed (trying to write something when it is closed)");
|
||||
throw new WrapperAlreadyDisposedException(e);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getLocator() {
|
||||
return this.locator;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,49 @@
|
|||
package org.gcube.data.spd.plugin;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import org.gcube.data.spd.model.KeyValue;
|
||||
import org.gcube.data.spd.model.PointInfo;
|
||||
import org.gcube.data.spd.model.binding.Bindings;
|
||||
import org.gcube.data.spd.model.products.OccurrencePoint;
|
||||
|
||||
|
||||
public class BindingTest {
|
||||
|
||||
public static void main(String[] args) throws Exception{
|
||||
occurrenceTest();
|
||||
}
|
||||
|
||||
static private String occurrencePoint = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?><occurrencePoint basisOfRecord=\"PreservedSpecimen\" minDepth=\"0.0\" maxDepth=\"0.0\" decimalLongitude=\"-59.167\" decimalLatitude=\"50.617\" country=\"Canada\" locality=\"\" scientificName=\"Carcharodon carcharias\" recordedBy=\"Mareoux, A.; Mareoux, C.\" catalogueNumber=\"CMNFI 1989-0126.1\" collectionCode=\"CMNFI\" institutionCode=\"CMN\" credits=\"Biodiversity occurrence data published by: Ocean Biogeographic Information System (Accessed through GBIF Data Portal, data.gbif.org, 2013-08-30)\" author=\"\" provider=\"\" id=\"17589157\"><dataSet id=\"344\"><citation>Canadian Museum of Nature - Fish Collection</citation><name>Canadian Museum of Nature - Fish Collection (OBIS Canada)</name><dataProvider id=\"82\"><name>Ocean Biogeographic Information System</name></dataProvider></dataSet></occurrencePoint>";
|
||||
|
||||
public static void pointInfoTest() throws Exception{
|
||||
PointInfo pi= new PointInfo(12.3, 15.5);
|
||||
|
||||
List<KeyValue> keyvaluelist= new ArrayList<KeyValue>();
|
||||
keyvaluelist.add(new KeyValue("test", "value"));
|
||||
|
||||
|
||||
//System.out.println(Arrays.toString(pi.getPropertiesList().toArray(new KeyValue[0])));
|
||||
|
||||
pi.setPropertiesList(keyvaluelist);
|
||||
System.out.println(Arrays.toString(pi.getPropertiesList().toArray(new KeyValue[0])));
|
||||
|
||||
String xml =Bindings.toXml(pi);
|
||||
System.out.println(xml);
|
||||
|
||||
PointInfo resPi = Bindings.fromXml(xml);
|
||||
|
||||
System.out.println(Arrays.toString(pi.getPropertiesList().toArray(new KeyValue[0])));
|
||||
}
|
||||
|
||||
|
||||
|
||||
public static void occurrenceTest() throws Exception{
|
||||
OccurrencePoint point = (OccurrencePoint)Bindings.fromXml(occurrencePoint);
|
||||
|
||||
System.out.println(Bindings.toXml(point));
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,18 @@
|
|||
# Set root category priority to WARN and its only appender to A1.
|
||||
log4j.rootCategory=TRACE, A1
|
||||
|
||||
log4j.appender.A1=org.apache.log4j.ConsoleAppender
|
||||
|
||||
# A2 uses PatternLayout.
|
||||
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
|
||||
log4j.appender.A1.layout.ConversionPattern=[CodelistManager] %d{HH:mm:ss,SSS} %-5p %c{2} [%t,%M:%L] %m%n
|
||||
|
||||
|
||||
|
||||
# Display any warnings generated by our code
|
||||
|
||||
log4j.category.org.gcube.data.spd=TRACE,A1
|
||||
log4j.category.org.gcube=INFO, A1
|
||||
log4j.additivity.org.gcube.data.spd=false
|
||||
|
||||
|
||||
Loading…
Reference in New Issue