org.gcube.portlets.user.speciesdiscovery.server.service

Class SpeciesService

java.lang.Object

org.gcube.portlets.user.speciesdiscovery.server.service.SpeciesService

public class SpeciesService
extends Object

The Class SpeciesService.

Author:

Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it Jan 10, 2017

Field Summary

Fields

Modifier and Type	Field and Description
protected org.gcube.data.spd.client.proxies.ManagerClient	call
protected org.gcube.data.spd.client.proxies.ClassificationClient	classificationCall
protected org.gcube.data.spd.client.proxies.ExecutorClient	executorCall
protected String	lastQuery
protected org.apache.log4j.Logger	logger
protected org.gcube.data.spd.client.proxies.OccurrenceClient	occurrencesCall
protected String	scope

Constructor Summary

Constructors

Constructor and Description
SpeciesService() Instantiates a new species service.
SpeciesService(String scope, boolean instanceOnlyOccurrence) Instantiates a new species service.

Method Summary

Modifier and Type	Method and Description
void	cancelGisLayerByJobId(String serverJobId) Cancel gis layer by job id.
void	cancelOccurrenceJobById(String jobIdentifier) Cancel occurrence job by id.
void	cancelTaxonomyJobById(String jobIdentifier) Cancel taxonomy job by id.
protected org.gcube.data.spd.model.Coordinate	convertCoordinate(Coordinate coordinate) Convert coordinate.
String	createOccurrenceCSVJob(org.gcube.data.streams.Stream<String> streamKey) Creates the occurrence csv job.
String	createOccurrenceCSVOpenModellerJob(org.gcube.data.streams.Stream<String> streamKey) Creates the occurrence csv open modeller job.
String	createOccurrenceDARWINCOREJob(org.gcube.data.streams.Stream<String> streamKey) Creates the occurrence darwincore job.
String	createTaxonomyJobForDWCAByChildren(String taxonomyId) Creates the taxonomy job for dwca by children.
String	createTaxonomyJobForDWCAByIds(List<String> ids) Creates the taxonomy job for dwca by ids.
String	generateGisLayerFromOccurrenceKeys(List<String> occurrenceKeys, String layerTitle, String layerDescr, String author, String credits) Generate gis layer from occurrence keys.
org.gcube.data.spd.model.service.types.CompleteJobStatus	getGisLayerByJobId(String serverJobId) Gets the gis layer by job id.
String	getGisLayerResultLinkByJobId(String serverJobId) Gets the gis layer result link by job id.
String	getLastQuery() Gets the last query.
org.gcube.data.spd.model.service.types.CompleteJobStatus	getOccurrenceJobById(String jobId) Gets the occurrence job by id.
InputStream	getOccurrenceJobErrorFileById(String jobIdentifier) Gets the occurrence job error file by id.
InputStream	getOccurrenceJobFileById(String jobIdentifier) Gets the occurrence job file by id.
CloseableIterator<org.gcube.data.spd.model.products.OccurrencePoint>	getOccurrencesByIds(List<String> ids) Gets the occurrences by ids.
CloseableIterator<org.gcube.data.spd.model.products.OccurrencePoint>	getOccurrencesByKeys(List<String> keys) Gets the occurrences by keys.
List<DataSourceModel>	getPlugins() Gets the plugins.
StreamIterator<org.gcube.data.spd.model.products.TaxonomyItem>	getTaxonChildrenByParentId(String parentId) Gets the taxon children by parent id.
org.gcube.data.spd.model.service.types.CompleteJobStatus	getTaxonomyJobById(String jobId) Gets the taxonomy job by id.
InputStream	getTaxonomyJobErrorFileById(String jobIdentifier) Gets the taxonomy job error file by id.
InputStream	getTaxonomyJobFileById(String jobIdentifier) Gets the taxonomy job file by id.
boolean	isAvailableOccurrenceJobErrorFileById(String jobIdentifier) Checks if is available occurrence job error file by id.
boolean	isAvailableTaxonomyJobErrorFileById(String jobIdentifier) Checks if is available taxonomy job error file by id.
CloseableIterator<org.gcube.data.spd.model.products.TaxonomyItem>	retrieveSynonymsById(String id) Retrieve synonyms by id.
CloseableIterator<org.gcube.data.spd.model.products.TaxonomyItem>	retrieveTaxonomyById(List<String> ids) Retrieve taxonomy by id.
CloseableIterator<org.gcube.data.spd.model.products.ResultElement>	searchByFilters(String searchTerm, SearchType searchType, SearchFilters searchFilters) Search by filters.
CloseableIterator<org.gcube.data.spd.model.products.ResultElement>	searchByQuery(String query) Search by query.
org.gcube.data.streams.Stream<org.gcube.data.spd.model.products.ResultElement>	searchByQuery2(String query) Search by query2.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logger

protected org.apache.log4j.Logger logger

scope

protected String scope

call

protected org.gcube.data.spd.client.proxies.ManagerClient call

occurrencesCall

protected org.gcube.data.spd.client.proxies.OccurrenceClient occurrencesCall

classificationCall

protected org.gcube.data.spd.client.proxies.ClassificationClient classificationCall

executorCall

protected org.gcube.data.spd.client.proxies.ExecutorClient executorCall

lastQuery

protected String lastQuery

Constructor Detail

SpeciesService

public SpeciesService()
               throws Exception

Instantiates a new species service.

Throws:

Exception - the exception

SpeciesService

public SpeciesService(String scope,
                      boolean instanceOnlyOccurrence)
               throws Exception

Instantiates a new species service.

Parameters:

scope - the scope

instanceOnlyOccurrence - the instance only occurrence

Throws:

Exception - the exception

Method Detail

searchByFilters

public CloseableIterator<org.gcube.data.spd.model.products.ResultElement> searchByFilters(String searchTerm,
                                                                                          SearchType searchType,
                                                                                          SearchFilters searchFilters)
                                                                                   throws SearchServiceException

Search by filters.

Parameters:

searchTerm - the search term

searchType - the search type

searchFilters - the search filters

Returns:

the closeable iterator

Throws:

SearchServiceException - the search service exception

retrieveTaxonomyById

public CloseableIterator<org.gcube.data.spd.model.products.TaxonomyItem> retrieveTaxonomyById(List<String> ids)
                                                                                       throws SearchServiceException

Retrieve taxonomy by id.

Parameters:

ids - the ids

Returns:

the closeable iterator

Throws:

SearchServiceException - the search service exception

retrieveSynonymsById

public CloseableIterator<org.gcube.data.spd.model.products.TaxonomyItem> retrieveSynonymsById(String id)
                                                                                       throws SearchServiceException

Retrieve synonyms by id.

Parameters:

id - the id

Returns:

the closeable iterator

Throws:

SearchServiceException - the search service exception

searchByQuery

public CloseableIterator<org.gcube.data.spd.model.products.ResultElement> searchByQuery(String query)
                                                                                 throws SearchServiceException

Search by query.

Parameters:

query - the query

Returns:

the closeable iterator

Throws:

SearchServiceException - the search service exception

searchByQuery2

public org.gcube.data.streams.Stream<org.gcube.data.spd.model.products.ResultElement> searchByQuery2(String query)
                                                                                              throws SearchServiceException

Search by query2.

Parameters:

query - the query

Returns:

the stream

Throws:

SearchServiceException - the search service exception

getPlugins

public List<DataSourceModel> getPlugins()
                                 throws SearchServiceException

Gets the plugins.

Returns:

the plugins

Throws:

SearchServiceException - the search service exception

convertCoordinate

protected org.gcube.data.spd.model.Coordinate convertCoordinate(Coordinate coordinate)

Convert coordinate.

Parameters:

coordinate - the coordinate

Returns:

the org.gcube.data.spd.model. coordinate

getOccurrencesByKeys

public CloseableIterator<org.gcube.data.spd.model.products.OccurrencePoint> getOccurrencesByKeys(List<String> keys)
                                                                                          throws SearchServiceException

Gets the occurrences by keys.

Parameters:

keys - the keys

Returns:

the occurrences by keys

Throws:

SearchServiceException - the search service exception

getOccurrencesByIds

public CloseableIterator<org.gcube.data.spd.model.products.OccurrencePoint> getOccurrencesByIds(List<String> ids)
                                                                                         throws SearchServiceException

Gets the occurrences by ids.

Parameters:

ids - the ids

Returns:

the occurrences by ids

Throws:

SearchServiceException - the search service exception

generateGisLayerFromOccurrenceKeys

public String generateGisLayerFromOccurrenceKeys(List<String> occurrenceKeys,
                                                 String layerTitle,
                                                 String layerDescr,
                                                 String author,
                                                 String credits)
                                          throws SearchServiceException

Generate gis layer from occurrence keys.

Parameters:

occurrenceKeys - the occurrence keys

layerTitle - the layer title

layerDescr - the layer descr

author - the author

credits - the credits

Returns:

the string

Throws:

SearchServiceException - the search service exception

getGisLayerByJobId

public org.gcube.data.spd.model.service.types.CompleteJobStatus getGisLayerByJobId(String serverJobId)
                                                                            throws InvalidJobIdException,
                                                                                   Exception

Gets the gis layer by job id.

Parameters:

serverJobId - the server job id

Returns:

the gis layer by job id

Throws:

InvalidJobIdException - the invalid job id exception

Exception - the exception

getGisLayerResultLinkByJobId

public String getGisLayerResultLinkByJobId(String serverJobId)
                                    throws InvalidJobIdException

Gets the gis layer result link by job id.

Parameters:

serverJobId - the server job id

Returns:

the gis layer result link by job id

Throws:

InvalidJobIdException - the invalid job id exception

cancelGisLayerByJobId

public void cancelGisLayerByJobId(String serverJobId)

Cancel gis layer by job id.

Parameters:

serverJobId - the server job id

getTaxonChildrenByParentId

public StreamIterator<org.gcube.data.spd.model.products.TaxonomyItem> getTaxonChildrenByParentId(String parentId)
                                                                                          throws Exception

Gets the taxon children by parent id.

Parameters:

parentId - the parent id

Returns:

the taxon children by parent id

Throws:

Exception - the exception

getTaxonomyJobById

public org.gcube.data.spd.model.service.types.CompleteJobStatus getTaxonomyJobById(String jobId)

Gets the taxonomy job by id.

Parameters:

jobId - the job id

Returns:

the taxonomy job by id

getTaxonomyJobFileById

public InputStream getTaxonomyJobFileById(String jobIdentifier)
                                   throws Exception

Gets the taxonomy job file by id.

Parameters:

jobIdentifier - the job identifier

Returns:

the taxonomy job file by id

Throws:

Exception - the exception

getTaxonomyJobErrorFileById

public InputStream getTaxonomyJobErrorFileById(String jobIdentifier)
                                        throws Exception

Gets the taxonomy job error file by id.

Parameters:

jobIdentifier - the job identifier

Returns:

the taxonomy job error file by id

Throws:

Exception - the exception

isAvailableTaxonomyJobErrorFileById

public boolean isAvailableTaxonomyJobErrorFileById(String jobIdentifier)
                                            throws Exception

Checks if is available taxonomy job error file by id.

Parameters:

jobIdentifier - the job identifier

Returns:

true, if is available taxonomy job error file by id

Throws:

Exception - the exception

createTaxonomyJobForDWCAByChildren

public String createTaxonomyJobForDWCAByChildren(String taxonomyId)
                                          throws Exception

Creates the taxonomy job for dwca by children.

Parameters:

taxonomyId - the taxonomy id

Returns:

the string

Throws:

Exception - the exception

createTaxonomyJobForDWCAByIds

public String createTaxonomyJobForDWCAByIds(List<String> ids)
                                     throws Exception

Creates the taxonomy job for dwca by ids.

Parameters:

ids - the ids

Returns:

the string

Throws:

Exception - the exception

cancelTaxonomyJobById

public void cancelTaxonomyJobById(String jobIdentifier)

Cancel taxonomy job by id.

Parameters:

jobIdentifier - the job identifier

getOccurrenceJobById

public org.gcube.data.spd.model.service.types.CompleteJobStatus getOccurrenceJobById(String jobId)

Gets the occurrence job by id.

Parameters:

jobId - the job id

Returns:

the occurrence job by id

createOccurrenceCSVJob

public String createOccurrenceCSVJob(org.gcube.data.streams.Stream<String> streamKey)
                              throws Exception

Creates the occurrence csv job.

Parameters:

streamKey - the stream key

Returns:

the string

Throws:

Exception - the exception

createOccurrenceDARWINCOREJob

public String createOccurrenceDARWINCOREJob(org.gcube.data.streams.Stream<String> streamKey)
                                     throws Exception

Creates the occurrence darwincore job.

Parameters:

streamKey - the stream key

Returns:

the string

Throws:

Exception - the exception

createOccurrenceCSVOpenModellerJob

public String createOccurrenceCSVOpenModellerJob(org.gcube.data.streams.Stream<String> streamKey)
                                          throws Exception

Creates the occurrence csv open modeller job.

Parameters:

streamKey - the stream key

Returns:

the string

Throws:

Exception - the exception

cancelOccurrenceJobById

public void cancelOccurrenceJobById(String jobIdentifier)

Cancel occurrence job by id.

Parameters:

jobIdentifier - the job identifier

getOccurrenceJobFileById

public InputStream getOccurrenceJobFileById(String jobIdentifier)
                                     throws Exception

Gets the occurrence job file by id.

Parameters:

jobIdentifier - the job identifier

Returns:

the occurrence job file by id

Throws:

Exception - the exception

getOccurrenceJobErrorFileById

public InputStream getOccurrenceJobErrorFileById(String jobIdentifier)
                                          throws Exception

Gets the occurrence job error file by id.

Parameters:

jobIdentifier - the job identifier

Returns:

the occurrence job error file by id

Throws:

Exception - the exception

isAvailableOccurrenceJobErrorFileById

public boolean isAvailableOccurrenceJobErrorFileById(String jobIdentifier)
                                              throws Exception

Checks if is available occurrence job error file by id.

Parameters:

jobIdentifier - the job identifier

Returns:

true, if is available occurrence job error file by id

Throws:

Exception - the exception

getLastQuery

public String getLastQuery()

Gets the last query.

Returns:

the last query