org.opentox.toxotis.core.component.qprf
Class QprfReport

java.lang.Object
  extended by org.opentox.toxotis.core.OTComponent<T>
      extended by org.opentox.toxotis.core.OTOnlineResource<T>
          extended by org.opentox.toxotis.core.OTPublishable<OTPublishable>
              extended by org.opentox.toxotis.core.component.qprf.QprfReport
All Implemented Interfaces:
Serializable, IOnlineResource, IOTComponent, IStAXWritable

public class QprfReport
extends OTPublishable<OTPublishable>
implements Serializable

Author:
Pantelis Sopasakis, Charalampos Chomenides
See Also:
Serialized Form

Field Summary
 
Fields inherited from class org.opentox.toxotis.core.OTOnlineResource
XSD_DATATYPE_LINKS
 
Fields inherited from class org.opentox.toxotis.core.OTComponent
meta, RDF_ABOUT, RDF_RDF, RDF_RESOURCE, RDF_TYPE
 
Constructor Summary
QprfReport()
           
QprfReport(VRI uri)
           
 
Method Summary
 com.hp.hpl.jena.ontology.Individual asIndividual(com.hp.hpl.jena.ontology.OntModel model)
          The OpenTox component as an individual.
 String getApplicabilityDomainResult()
           
 Set<QprfAuthor> getAuthors()
           
 Compound getCompound()
           
 String getDoAName()
           
 String getDoaUri()
           
 String getExperimentalResult()
           
 List<String> getExperimentalValues()
           
 String getExpResultUnits()
           
 String getKeyword()
           
 Model getModel()
           
 Long getModelDate()
           
 String getPredictionResult()
           
 String getPredResultUnits()
           
 String getQMRFreference()
           
 Long getReportDate()
           
 QprfReportMeta getReportMeta()
           
 double getSimilarityLevel()
           
 List<Compound> getStructuralAnalogues()
           
protected  OTPublishable loadFromRemote(VRI vri, AuthenticationToken token)
          Loads an OpenTox component from a remote location identified by its uri and parses it into an instance of T.
 Task publishOnline(AuthenticationToken token)
          Publish the component to a standard (default) server.
 Task publishOnline(VRI vri, AuthenticationToken token)
          Publish the component to a proper server identified by the uri of the publishing service provided in this method.
 QprfReport setApplicabilityDomainResult(String applicabilityDomainResult)
           
 QprfReport setAuthors(Set<QprfAuthor> authors)
           
 QprfReport setCompound(Compound compound)
           
 void setDoAName(String doAName)
           
 QprfReport setDoaUri(String doaUri)
           
 QprfReport setExperimentalResult(String experimentalResult)
           
 void setExperimentalValues(List<String> experimentalValues)
           
 QprfReport setExpResultUnits(String expResultUnits)
           
 QprfReport setKeyword(String keywords)
           
 void setModel(Model model)
           
 QprfReport setModelDate(long model_date)
           
 QprfReport setPredictionResult(String predictionResult)
           
 QprfReport setPredResultUnits(String predResultUnits)
           
 QprfReport setQMRFreference(String QMRFreference)
           
 QprfReport setReportDate(long report_date)
           
 void setReportMeta(QprfReportMeta reportMeta)
           
 QprfReport setSimilarityLevel(double similarityLevel)
           
 void setStructuralAnalogues(List<Compound> structuralAnalogues)
           
 void writeRdf(XMLStreamWriter writer)
          Due to the large size of some objects like datasets, it is advisable to use this method for serializing large objects to RDF/XML rather than the method OntModel#write(OutputStream).
 
Methods inherited from class org.opentox.toxotis.core.OTPublishable
publish, publish
 
Methods inherited from class org.opentox.toxotis.core.OTOnlineResource
download, download, download, download, downloadImage, loadFromRemote, loadFromRemote
 
Methods inherited from class org.opentox.toxotis.core.OTComponent
addOntologicalClasses, asOntModel, endRdfWriter, equals, getMeta, getOntologicalClasses, getUri, hashCode, initRdfWriter, isEnabled, setEnabled, setMeta, setOntologicalClasses, setUri, writeAnnotationProperty, writeClass, writeDatatypeProperty, writeMetaDataProperties, writeObjectProperty, writeRdf, writeRdf, writeSuperClassRelationships
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.opentox.toxotis.core.IOTComponent
addOntologicalClasses, asOntModel, getMeta, getOntologicalClasses, getUri, isEnabled, setEnabled, setMeta, setOntologicalClasses
 

Constructor Detail

QprfReport

public QprfReport()

QprfReport

public QprfReport(VRI uri)
Method Detail

getReportMeta

public QprfReportMeta getReportMeta()

setReportMeta

public void setReportMeta(QprfReportMeta reportMeta)

getQMRFreference

public String getQMRFreference()

setQMRFreference

public QprfReport setQMRFreference(String QMRFreference)

getApplicabilityDomainResult

public String getApplicabilityDomainResult()

setApplicabilityDomainResult

public QprfReport setApplicabilityDomainResult(String applicabilityDomainResult)

getAuthors

public Set<QprfAuthor> getAuthors()

setAuthors

public QprfReport setAuthors(Set<QprfAuthor> authors)

getDoaUri

public String getDoaUri()

setDoaUri

public QprfReport setDoaUri(String doaUri)

getExperimentalResult

public String getExperimentalResult()

setExperimentalResult

public QprfReport setExperimentalResult(String experimentalResult)

getKeyword

public String getKeyword()

setKeyword

public QprfReport setKeyword(String keywords)

getModelDate

public Long getModelDate()

setModelDate

public QprfReport setModelDate(long model_date)

getPredictionResult

public String getPredictionResult()

setPredictionResult

public QprfReport setPredictionResult(String predictionResult)

getReportDate

public Long getReportDate()

setReportDate

public QprfReport setReportDate(long report_date)

publishOnline

public Task publishOnline(VRI vri,
                          AuthenticationToken token)
                   throws ServiceInvocationException
Description copied from class: OTPublishable
Publish the component to a proper server identified by the uri of the publishing service provided in this method. The resource will be posted to the server in RDF format (application/rdf+xml).

Specified by:
publishOnline in class OTPublishable<OTPublishable>
Parameters:
vri - URI of the service that is responsible for the publication of this kind of resources.
token - Provide an authentication token. If you think that the service does not require auhtentication/authorization, you can leave this field null or you can provide an empty authentication token. If the provided URI already contains an authentication token (as the URL parameter tokenid) it will be replaced by the new token provided to this method.
Returns:
A Task for monitoring the progress of your request. If the service returns the URI of the resource right away and does not return a task, then the object you will receive from this method will now have an identifier, its status will be set to Completed, its progress will be set to 100% and the URI of the created resource will be available applying the method Task.getResultUri() on the returned task. In any case, the service's response will be wrapped in a Task object.
Throws:
ServiceInvocationException

publishOnline

public Task publishOnline(AuthenticationToken token)
                   throws ServiceInvocationException
Description copied from class: OTPublishable
Publish the component to a standard (default) server. The resource will be posted to the server in RDF format (application/rdf+xml). If you want to specify at which server the resource should be posted, use the other method.

Specified by:
publishOnline in class OTPublishable<OTPublishable>
Parameters:
token - Provide an authentication token. If you think that the service does not require auhtentication/authorization, you can leave this field null or you can provide an empty authentication token.If the provided URI already contains an authentication token (as the URL parameter tokenid) it will be replaced by the new token provided to this method.
Returns:
A Task for monitoring the progress of your request. If the service returns the URI of the resource right away and does not return a task, then the object you will receive from this method will now have an identifier, its status will be set to Completed, its progress will be set to 100% and the URI of the created resource will be available applying the method Task.getResultUri() on the returned task. In any case, the service's response will be wrapped in a Task object.
Throws:
ServiceInvocationException - In case of invalid credentials, if the POSTed resource is not acceptable by the remote service (returns a status code 400), communication error occur with the remote server or other connection problems or the access to the service was denied (401 or 403).
See Also:
alternative method

loadFromRemote

protected OTPublishable loadFromRemote(VRI vri,
                                       AuthenticationToken token)
                                throws ServiceInvocationException
Description copied from class: OTOnlineResource
Loads an OpenTox component from a remote location identified by its uri and parses it into an instance of T. This method is protected and should be implemented by all subclasses of OTOnlineResource. The method is invoked by its public counterpart OTOnlineResource.loadFromRemote(org.opentox.toxotis.util.aa.AuthenticationToken) which accesses the remote location providing an authentication token.

Specified by:
loadFromRemote in class OTOnlineResource<OTPublishable>
Parameters:
vri - Identifier of the location from where the component should be downloaded and parsed
token - Token provided
Returns:
Parsed instance of the component.
Throws:
ServiceInvocationException

asIndividual

public com.hp.hpl.jena.ontology.Individual asIndividual(com.hp.hpl.jena.ontology.OntModel model)
Description copied from interface: IOTComponent
The OpenTox component as an individual.

Specified by:
asIndividual in interface IOTComponent
Parameters:
model - The ontological model to which the individual belongs.
Returns:
The OpenTox component as an individual of a data model.

writeRdf

public void writeRdf(XMLStreamWriter writer)
              throws XMLStreamException
Description copied from interface: IStAXWritable
Due to the large size of some objects like datasets, it is advisable to use this method for serializing large objects to RDF/XML rather than the method OntModel#write(OutputStream). In the case of Datasets, it has been shown that this method performs much faster (about 7,5 times faster on a dataset of 21 features and 1000 compounds).

Specified by:
writeRdf in interface IStAXWritable
Parameters:
writer - XML Stream Writer used for the serialization of the dataset object.
Throws:
XMLStreamException - In case the serialization is not possible due to syntax errors.

getCompound

public Compound getCompound()

setCompound

public QprfReport setCompound(Compound compound)

getModel

public Model getModel()

setModel

public void setModel(Model model)

getStructuralAnalogues

public List<Compound> getStructuralAnalogues()

setStructuralAnalogues

public void setStructuralAnalogues(List<Compound> structuralAnalogues)

getDoAName

public String getDoAName()

setDoAName

public void setDoAName(String doAName)

getSimilarityLevel

public double getSimilarityLevel()

setSimilarityLevel

public QprfReport setSimilarityLevel(double similarityLevel)

getExpResultUnits

public String getExpResultUnits()

setExpResultUnits

public QprfReport setExpResultUnits(String expResultUnits)

getPredResultUnits

public String getPredResultUnits()

setPredResultUnits

public QprfReport setPredResultUnits(String predResultUnits)

getExperimentalValues

public List<String> getExperimentalValues()

setExperimentalValues

public void setExperimentalValues(List<String> experimentalValues)


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