gCubeSystem
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species-products-discovery
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git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/branches/data-access/species-products-discovery/3.0@142784 82a268e6-3cf1-43bd-a215-b396298e98cf

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master
Lucio Lelii 7 years ago
parent a6d170627b
commit 9e57374771
7 changed files with 84 additions and 55 deletions
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5
pom.xml
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@ -252,11 +252,12 @@
<!-- <plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.4</version>
<configuration>
<warName>species-products-discovery</warName>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin> -->
</plugin> -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
@ -278,4 +279,6 @@
</plugin>
</plugins>
</build>
</project>

11
src/main/java/org/gcube/data/spd/resources/Classification.java
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@ -13,6 +13,7 @@ import javax.ws.rs.Path;
import javax.ws.rs.PathParam;
import javax.ws.rs.core.Response;
import org.gcube.common.resources.gcore.GCoreEndpoint;
import org.gcube.data.spd.exception.MaxRetriesReachedException;
import org.gcube.data.spd.manager.AppInitializer;
import org.gcube.data.spd.manager.TaxonomyItemWriterManager;
@ -26,6 +27,7 @@ import org.gcube.data.spd.model.products.TaxonomyItem;
import org.gcube.data.spd.model.service.exceptions.InvalidIdentifierException;
import org.gcube.data.spd.model.service.exceptions.UnsupportedCapabilityException;
import org.gcube.data.spd.model.service.exceptions.UnsupportedPluginException;
import org.gcube.data.spd.model.service.types.MultiLocatorResponse;
import org.gcube.data.spd.model.util.Capabilities;
import org.gcube.data.spd.plugin.PluginManager;
import org.gcube.data.spd.plugin.fwk.AbstractPlugin;
@ -89,7 +91,8 @@ public class Classification {
redirectUri.append(ctx.application().getContextPath()).append(Constants.APPLICATION_ROOT_PATH).append("/").append(Constants.RESULTSET_PATH).append("/").append(wrapper.getLocator());
logger.trace("redirect uri is {} ",redirectUri.toString());
try{
return Response.temporaryRedirect(new URI(redirectUri.toString())).build();
MultiLocatorResponse multiLocatorResponse = new MultiLocatorResponse( wrapper.getLocator(), null, ctx.profile(GCoreEndpoint.class).id());
return Response.temporaryRedirect(new URI(redirectUri.toString())).entity(multiLocatorResponse).build();
}catch(Exception e){
logger.error("invalid redirect uri created",e);
return Response.serverError().build();
@ -138,7 +141,8 @@ public class Classification {
redirectUri.append(ctx.application().getContextPath()).append(Constants.APPLICATION_ROOT_PATH).append("/").append(Constants.RESULTSET_PATH).append("/").append(wrapper.getLocator());
logger.trace("redirect uri is {} ",redirectUri.toString());
try{
return Response.temporaryRedirect(new URI(redirectUri.toString())).build();
MultiLocatorResponse multiLocatorResponse = new MultiLocatorResponse(wrapper.getLocator(), null, ctx.profile(GCoreEndpoint.class).id());
return Response.temporaryRedirect(new URI(redirectUri.toString())).entity(multiLocatorResponse).build();
}catch(Exception e){
logger.error("invalid redirect uri created",e);
return Response.serverError().build();
@ -193,7 +197,8 @@ public class Classification {
redirectUri.append(ctx.application().getContextPath()).append(Constants.APPLICATION_ROOT_PATH).append("/").append(Constants.RESULTSET_PATH).append("/").append(wrapper.getLocator());
logger.trace("redirect uri is {} ",redirectUri.toString());
try{
return Response.temporaryRedirect(new URI(redirectUri.toString())).build();
MultiLocatorResponse multiLocatorResponse = new MultiLocatorResponse(null, wrapper.getLocator(), ctx.profile(GCoreEndpoint.class).id());
return Response.temporaryRedirect(new URI(redirectUri.toString())).entity(multiLocatorResponse).build();
}catch(Exception e){
logger.error("invalid redirect uri created",e);
return Response.serverError().build();

43
src/main/java/org/gcube/data/spd/resources/Executor.java
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@ -16,11 +16,12 @@ import javax.ws.rs.Consumes;
import javax.ws.rs.DELETE;
import javax.ws.rs.GET;
import javax.ws.rs.POST;
import javax.ws.rs.PUT;
import javax.ws.rs.Path;
import javax.ws.rs.PathParam;
import javax.ws.rs.Produces;
import javax.ws.rs.core.MediaType;
import org.gcube.common.resources.gcore.GCoreEndpoint;
import org.gcube.common.resources.gcore.HostingNode;
import org.gcube.data.spd.executor.jobs.SpeciesJob;
import org.gcube.data.spd.executor.jobs.URLJob;
@ -39,9 +40,8 @@ import org.gcube.data.spd.model.service.types.CompleteJobStatus;
import org.gcube.data.spd.model.service.types.JobStatus;
import org.gcube.data.spd.model.service.types.NodeStatus;
import org.gcube.data.spd.model.service.types.SubmitJob;
import org.gcube.data.spd.model.util.SerializableList;
import org.gcube.data.spd.model.service.types.SubmitJobResponse;
import org.gcube.data.spd.plugin.PluginManager;
import org.gcube.data.spd.utils.DynamicList;
import org.gcube.data.spd.utils.DynamicMap;
import org.gcube.data.spd.utils.ExecutorsContainer;
import org.gcube.smartgears.ApplicationManagerProvider;
@ -204,35 +204,6 @@ public class Executor {
}
@PUT
@Path("input/{jobKey}")
@Consumes(MediaType.APPLICATION_XML)
public boolean submitJob(@PathParam("jobKey") String jobKey, SerializableList<String> input) throws InvalidIdentifierException {
//String node;
String jobId;
try{
//node = extractNode(jobKey);
jobId = extractId(jobKey);
}catch (IdNotValidException e) {
logger.error("id not valid "+jobKey,e);
throw new InvalidIdentifierException(jobKey);
}
logger.trace("job Id extracted is {} ",jobId);
if (input.getValuesList().isEmpty()){
logger.info("closing input stream");
DynamicMap.remove(jobId);
}
else {
DynamicList list = DynamicMap.get(jobId);
for (String id : input.getValuesList()){
logger.trace("elaborating input id ",id);
if (!list.add(id)) return false;
}
}
return true;
}
@DELETE
@Path("{jobKey}")
public void removeJob(@PathParam("jobKey") String jobId) throws InvalidIdentifierException {
@ -244,7 +215,8 @@ public class Executor {
@POST
@Path("execute")
@Consumes(MediaType.APPLICATION_XML)
public String submitJob(SubmitJob request) throws InvalidJobException {
@Produces(MediaType.APPLICATION_XML)
public SubmitJobResponse submitJob(SubmitJob request) throws InvalidJobException {
PluginManager pluginManger = initializer.getPluginManager();
SpeciesJob job = null;
switch (request.getJob()) {
@ -277,7 +249,10 @@ public class Executor {
if (job ==null || !job.validateInput(request.getInput()))
throw new InvalidJobException();
return executeJob(job);
String jobId = executeJob(job);
return new SubmitJobResponse(job.getId(), jobId, cxt.profile(GCoreEndpoint.class).id());
}

5
src/main/java/org/gcube/data/spd/resources/Manager.java
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@ -16,6 +16,7 @@ import javax.ws.rs.QueryParam;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import org.gcube.common.resources.gcore.GCoreEndpoint;
import org.gcube.data.spd.caching.QueryCacheFactory;
import org.gcube.data.spd.manager.AppInitializer;
import org.gcube.data.spd.manager.OccurrenceWriterManager;
@ -34,6 +35,7 @@ import org.gcube.data.spd.model.products.TaxonomyItem;
import org.gcube.data.spd.model.service.exceptions.QueryNotValidException;
import org.gcube.data.spd.model.service.exceptions.UnsupportedCapabilityException;
import org.gcube.data.spd.model.service.exceptions.UnsupportedPluginException;
import org.gcube.data.spd.model.service.types.MultiLocatorResponse;
import org.gcube.data.spd.model.service.types.PluginDescriptions;
import org.gcube.data.spd.model.util.Capabilities;
import org.gcube.data.spd.plugin.PluginManager;
@ -177,7 +179,8 @@ public class Manager {
redirectUri.append(ctx.application().getContextPath()).append(Constants.APPLICATION_ROOT_PATH).append("/").append(Constants.RESULTSET_PATH).append("/").append(locator);
logger.trace("redirect uri is {} ",redirectUri.toString());
try{
return Response.temporaryRedirect(new URI(redirectUri.toString())).build();
MultiLocatorResponse multiLocatorResponse = new MultiLocatorResponse(locator, null, ctx.profile(GCoreEndpoint.class).id());
return Response.temporaryRedirect(new URI(redirectUri.toString())).entity(multiLocatorResponse).build();
}catch(Exception e){
logger.error("invalid redirect uri created",e);
return Response.serverError().build();

37
src/main/java/org/gcube/data/spd/resources/Occurrences.java
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@ -1,16 +1,18 @@
package org.gcube.data.spd.resources;
import static org.gcube.data.streams.dsl.Streams.convert;
import java.net.URI;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import javax.ws.rs.GET;
import javax.ws.rs.Path;
import javax.ws.rs.QueryParam;
import javax.ws.rs.core.Response;
import org.gcube.common.authorization.library.AuthorizedTasks;
import org.gcube.common.resources.gcore.GCoreEndpoint;
import org.gcube.data.spd.exception.MaxRetriesReachedException;
import org.gcube.data.spd.manager.AppInitializer;
import org.gcube.data.spd.manager.OccurrenceWriterManager;
@ -19,6 +21,7 @@ import org.gcube.data.spd.model.exceptions.ExternalRepositoryException;
import org.gcube.data.spd.model.exceptions.IdNotValidException;
import org.gcube.data.spd.model.exceptions.StreamBlockingException;
import org.gcube.data.spd.model.products.OccurrencePoint;
import org.gcube.data.spd.model.service.types.MultiLocatorResponse;
import org.gcube.data.spd.plugin.PluginManager;
import org.gcube.data.spd.plugin.fwk.AbstractPlugin;
import org.gcube.data.spd.plugin.fwk.capabilities.OccurrencesCapability;
@ -28,12 +31,12 @@ import org.gcube.data.spd.plugin.fwk.writers.Writer;
import org.gcube.data.spd.plugin.fwk.writers.rswrapper.AbstractWrapper;
import org.gcube.data.spd.plugin.fwk.writers.rswrapper.LocalWrapper;
import org.gcube.data.spd.plugin.fwk.writers.rswrapper.ResultWrapper;
import org.gcube.data.spd.utils.DynamicMap;
import org.gcube.data.spd.utils.ExecutorsContainer;
import org.gcube.data.spd.utils.QueryRetryCall;
import org.gcube.data.spd.utils.ResultWrapperMantainer;
import org.gcube.data.spd.utils.VOID;
import org.gcube.data.streams.Stream;
import org.gcube.data.streams.dsl.Streams;
import org.gcube.smartgears.ApplicationManagerProvider;
import org.gcube.smartgears.ContextProvider;
import org.gcube.smartgears.context.application.ApplicationContext;
@ -57,16 +60,18 @@ public class Occurrences{
@GET
@Path("keys")
public Response getByKeys(@QueryParam("keys") List<String> keys) {
public Response getByKeys() {
try{
logger.trace("keys arrived are {} ",keys);
Stream<String> reader = Streams.convert(keys.iterator());
String inputLocatorId = UUID.randomUUID().toString();
DynamicMap.put(inputLocatorId);
logger.trace("locator used as input is {} ",inputLocatorId);
Stream<String> reader = convert(DynamicMap.get(inputLocatorId));
ResultWrapper<OccurrencePoint> wrapper = ResultWrapperMantainer.getWrapper(OccurrencePoint.class);
logger.trace("entering in the getOccurrence by productKeys with keys {}",keys);
ExecutorsContainer.execJob(AuthorizedTasks.bind(new RunnableOccurrenceSearch(reader, wrapper, ExecType.KEYS)));
// the output will be probably returned even before
@ -74,9 +79,12 @@ public class Occurrences{
StringBuilder redirectUri = new StringBuilder();
redirectUri.append("http://").append(ctx.container().configuration().hostname()).append(":").append(ctx.container().configuration().port());
redirectUri.append(ctx.application().getContextPath()).append(Constants.APPLICATION_ROOT_PATH).append("/").append(Constants.RESULTSET_PATH).append("/").append(wrapper.getLocator());
logger.trace("redirect uri is {} ",redirectUri.toString());
try{
return Response.temporaryRedirect(new URI(redirectUri.toString())).build();
MultiLocatorResponse multiLocatorResponse = new MultiLocatorResponse(wrapper.getLocator(), inputLocatorId, ctx.profile(GCoreEndpoint.class).id());
logger.trace("retrnign multilocator {}",multiLocatorResponse);
return Response.temporaryRedirect(new URI(redirectUri.toString())).entity(multiLocatorResponse).build();
}catch(Exception e){
logger.error("invalid redirect uri created",e);
return Response.serverError().build();
@ -89,9 +97,13 @@ public class Occurrences{
@GET
@Path("ids")
public Response getByIds(@QueryParam("ids") List<String> ids){
public Response getByIds(){
try{
Stream<String> reader = Streams.convert(ids.iterator());
String inputLocatorId = UUID.randomUUID().toString();
DynamicMap.put(inputLocatorId);
Stream<String> reader = convert(DynamicMap.get(inputLocatorId));
ResultWrapper<OccurrencePoint> wrapper = ResultWrapperMantainer.getWrapper(OccurrencePoint.class);
ExecutorsContainer.execJob(AuthorizedTasks.bind(new RunnableOccurrenceSearch(reader, wrapper, ExecType.IDS)));
@ -102,7 +114,8 @@ public class Occurrences{
redirectUri.append(ctx.application().getContextPath()).append(Constants.APPLICATION_ROOT_PATH).append("/").append(Constants.RESULTSET_PATH).append("/").append(wrapper.getLocator());
logger.trace("redirect uri is {} ",redirectUri.toString());
try{
return Response.temporaryRedirect(new URI(redirectUri.toString())).build();
MultiLocatorResponse multiLocatorResponse = new MultiLocatorResponse(wrapper.getLocator(), inputLocatorId, ctx.profile(GCoreEndpoint.class).id());
return Response.temporaryRedirect(new URI(redirectUri.toString())).entity(multiLocatorResponse).build();
}catch(Exception e){
logger.error("invalid redirect uri created",e);
return Response.serverError().build();

34
src/main/java/org/gcube/data/spd/resources/ResultSetEndpoint.java
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@ -1,13 +1,19 @@
package org.gcube.data.spd.resources;
import javax.ws.rs.Consumes;
import javax.ws.rs.DELETE;
import javax.ws.rs.GET;
import javax.ws.rs.PUT;
import javax.ws.rs.Path;
import javax.ws.rs.PathParam;
import javax.ws.rs.Produces;
import javax.ws.rs.core.MediaType;
import org.gcube.data.spd.model.Constants;
import org.gcube.data.spd.model.service.exceptions.InvalidIdentifierException;
import org.gcube.data.spd.model.util.SerializableList;
import org.gcube.data.spd.utils.DynamicList;
import org.gcube.data.spd.utils.DynamicMap;
import org.gcube.data.spd.utils.ResultWrapperMantainer;
import org.glassfish.jersey.server.ChunkedOutput;
import org.slf4j.Logger;
@ -17,8 +23,8 @@ import org.slf4j.LoggerFactory;
@Path(value = Constants.RESULTSET_PATH)
public class ResultSetEndpoint {
Logger logger = LoggerFactory.getLogger(ResultSetEndpoint.class);
private static Logger logger = LoggerFactory.getLogger(ResultSetEndpoint.class);
@GET
@Produces(MediaType.TEXT_XML)
@Path("{locator}")
@ -35,4 +41,28 @@ public class ResultSetEndpoint {
ResultWrapperMantainer.remove(locator);
}
@PUT
@Consumes(MediaType.APPLICATION_XML)
@Path("{locator}")
public boolean sendInput(@PathParam("locator") String id, SerializableList<String> input) throws InvalidIdentifierException {
//String node;
DynamicList list = DynamicMap.get(id);
if (list==null){
logger.error("id not valid "+id);
throw new InvalidIdentifierException(id);
}
logger.trace("input id is {} ",id);
if (input.getValuesList().isEmpty()){
logger.info("closing input stream");
DynamicMap.remove(id);
}
else {
for (String singleInput : input.getValuesList()){
logger.trace("elaborating input",singleInput);
if (!list.add(singleInput)) return false;
}
}
return true;
}
}

4
src/main/java/org/gcube/data/spd/utils/DynamicList.java
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@ -11,8 +11,8 @@ public class DynamicList implements Iterator<String>{
private static Logger logger = LoggerFactory.getLogger(DynamicList.class);
private final static long TIMEOUT_IN_MILLIS = 1000;
private final static int RETRY = 10;
private final static long TIMEOUT_IN_MILLIS = 2000;
private final static int RETRY = 20;
private LinkedBlockingQueue<String> internalQueue = new LinkedBlockingQueue<String>(50);

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