Uses of Class
com.genologics.ri.file.ClarityFile

Packages that use ClarityFile

Package	Description
com.genologics.ri.artifact	Provides JAXB bindings for artifacts in the Genologics REST API.
com.genologics.ri.automation	Entities for automation resources in the Clarity system.
com.genologics.ri.file	Entities for file resources in the Clarity system.
com.genologics.ri.process	Entities for processes executed in the Clarity system.
com.genologics.ri.processtype	Entities for process type definitions in the Clarity system.
com.genologics.ri.project	Project entity and supporting classes for the Clarity REST API.
com.genologics.ri.sample	Provides classes for sample entities in the Clarity LIMS API.
org.cruk.clarity.api	The main public package of the Clarity API.
org.cruk.clarity.api.cache	Package supporting caching of Clarity entities in memory (or, if so configured, on disk) to reduce the amount of traffic being sent to and from the REST API.
org.cruk.clarity.api.filestore	Top level package for SFTP file store providers for the API.
org.cruk.clarity.api.impl	Concrete implementation classes of the Clarity API.

Uses of ClarityFile in com.genologics.ri.artifact

Fields in com.genologics.ri.artifact declared as ClarityFile

Modifier and Type	Field	Description
protected ClarityFile	Artifact.file	The file associated with this artifact, if any.

Methods in com.genologics.ri.artifact that return ClarityFile

Modifier and Type	Method	Description
ClarityFile	Artifact.getFile()	File provides a URI linking to the detailed representation of the File associated with the Artifact.

Methods in com.genologics.ri.artifact with parameters of type ClarityFile

Modifier and Type	Method	Description
void	Artifact.setFile(ClarityFile value)	Sets the file associated with this artifact.

Uses of ClarityFile in com.genologics.ri.automation

Fields in com.genologics.ri.automation with type parameters of type ClarityFile

Modifier and Type	Field	Description
protected List<ClarityFile>	Automation.files	The files associated with this automation.

Methods in com.genologics.ri.automation that return types with arguments of type ClarityFile

Modifier and Type	Method	Description
List<ClarityFile>	Automation.getFiles()	Gets the list of files associated with this automation.

Uses of ClarityFile in com.genologics.ri.file

Fields in com.genologics.ri.file with type parameters of type ClarityFile

Modifier and Type	Field	Description
protected List<ClarityFile>	ClarityFileBatchFetchResult.files	The list of file resources in this batch.

Methods in com.genologics.ri.file that return ClarityFile

Modifier and Type	Method	Description
ClarityFile	ObjectFactory.createFile()	Creates a new instance of ClarityFile.

Methods in com.genologics.ri.file that return types with arguments of type ClarityFile

Modifier and Type	Method	Description
JAXBElement<ClarityFile>	ObjectFactory.createFile(ClarityFile value)	Creates a JAXBElement wrapping a ClarityFile instance.
Class<ClarityFile>	ClarityFile.getEntityClass()	Gets the entity class for this file.
Class<ClarityFile>	FileLink.getEntityClass()	Gets the entity class that this link references.
List<ClarityFile>	ClarityFileBatchFetchResult.getFiles()	Gets the list of files in this batch.
List<ClarityFile>	ClarityFileBatchFetchResult.getList()	Gets the list of files in this batch.

Methods in com.genologics.ri.file with parameters of type ClarityFile

Modifier and Type	Method	Description
JAXBElement<ClarityFile>	ObjectFactory.createFile(ClarityFile value)	Creates a JAXBElement wrapping a ClarityFile instance.

Method parameters in com.genologics.ri.file with type arguments of type ClarityFile

Modifier and Type	Method	Description
void	ClarityFileBatchFetchResult.addForCreate(Collection<ClarityFile> entities)	Adds a collection of file entities to this batch for creation.
void	ClarityFileBatchFetchResult.addForUpdate(Collection<ClarityFile> entities)	Adds a collection of file entities to this batch for update.

Constructors in com.genologics.ri.file with parameters of type ClarityFile

Modifier	Constructor	Description
	ClarityFile(ClarityFile file)	Creates a new ClarityFile as a copy of another ClarityFile, copying its URI and LIMS id.

Constructor parameters in com.genologics.ri.file with type arguments of type ClarityFile

Modifier	Constructor	Description
	FileLink(LimsEntityLinkable<ClarityFile> link)	Creates a new FileLink from a linkable entity that references a ClarityFile, copying its URI and LIMS id.

Uses of ClarityFile in com.genologics.ri.process

Fields in com.genologics.ri.process with type parameters of type ClarityFile

Modifier and Type	Field	Description
protected List<ClarityFile>	ClarityProcess.files	The files associated with the process.

Methods in com.genologics.ri.process that return ClarityFile

Modifier and Type	Method	Description
ClarityFile	ClarityProcess.addFile(ClarityFile f)	Adds a file to the process.

Methods in com.genologics.ri.process that return types with arguments of type ClarityFile

Modifier and Type	Method	Description
List<ClarityFile>	ClarityProcess.getFiles()	Gets the files associated with the process.

Methods in com.genologics.ri.process with parameters of type ClarityFile

Modifier and Type	Method	Description
ClarityFile	ClarityProcess.addFile(ClarityFile f)	Adds a file to the process.

Uses of ClarityFile in com.genologics.ri.processtype

Fields in com.genologics.ri.processtype with type parameters of type ClarityFile

Modifier and Type	Field	Description
protected List<ClarityFile>	Parameter.files	Files associated with this parameter.

Methods in com.genologics.ri.processtype that return types with arguments of type ClarityFile

Modifier and Type	Method	Description
List<ClarityFile>	Parameter.getFiles()	Each File provides a URI linking to the detailed representation of a File associated with the Process Parameter.

Uses of ClarityFile in com.genologics.ri.project

Fields in com.genologics.ri.project with type parameters of type ClarityFile

Modifier and Type	Field	Description
protected List<ClarityFile>	Project.files	The files attached to the project.

Methods in com.genologics.ri.project that return ClarityFile

Modifier and Type	Method	Description
ClarityFile	Project.addFile(ClarityFile f)	Add a file to the project.

Methods in com.genologics.ri.project that return types with arguments of type ClarityFile

Modifier and Type	Method	Description
List<ClarityFile>	Project.getFiles()	Get the files attached to the project.

Methods in com.genologics.ri.project with parameters of type ClarityFile

Modifier and Type	Method	Description
ClarityFile	Project.addFile(ClarityFile f)	Add a file to the project.

Uses of ClarityFile in com.genologics.ri.sample

Fields in com.genologics.ri.sample with type parameters of type ClarityFile

Modifier and Type	Field	Description
protected List<ClarityFile>	SampleBase.files	The files associated with this sample.

Methods in com.genologics.ri.sample that return ClarityFile

Modifier and Type	Method	Description
ClarityFile	SampleBase.addFile(ClarityFile f)	Adds a file to this sample.

Methods in com.genologics.ri.sample that return types with arguments of type ClarityFile

Modifier and Type	Method	Description
List<ClarityFile>	SampleBase.getFiles()	Gets the list of files associated with this sample.

Methods in com.genologics.ri.sample with parameters of type ClarityFile

Modifier and Type	Method	Description
ClarityFile	SampleBase.addFile(ClarityFile f)	Adds a file to this sample.

Uses of ClarityFile in org.cruk.clarity.api

Methods in org.cruk.clarity.api that return ClarityFile

Modifier and Type	Method	Description
<E extends LimsEntity<E>> ClarityFile	ClarityAPI.uploadFile(LimsEntityLinkable<E> entity, URL fileURL, boolean publishInLablink)	Attach a file to an entity and upload that file to the file store.

Method parameters in org.cruk.clarity.api with type arguments of type ClarityFile

Modifier and Type	Method	Description
void	ClarityAPI.deleteAndRemoveFile(Linkable<ClarityFile> file)	Delete a file from the file store and remove its record from the LIMS.
void	ClarityAPI.downloadFile(Linkable<ClarityFile> file, OutputStream resultStream)	Download the given file from its source.

Uses of ClarityFile in org.cruk.clarity.api.cache

Methods in org.cruk.clarity.api.cache that return ClarityFile

Modifier and Type	Method	Description
ClarityFile	ClarityAPICache.uploadFile(org.aspectj.lang.ProceedingJoinPoint pjp)	Join point for the ClarityAPI.uploadFile method.

Uses of ClarityFile in org.cruk.clarity.api.filestore

Methods in org.cruk.clarity.api.filestore with parameters of type ClarityFile

Modifier and Type	Method	Description
void	ClaritySFTPUploader.delete(ClarityFile targetFile)	Delete a file from the Clarity file store.
void	ClaritySFTPUploader.upload(URLInputStreamResource fileURLResource, ClarityFile targetFile)	Upload a file to the Clarity file store.

Uses of ClarityFile in org.cruk.clarity.api.impl

Methods in org.cruk.clarity.api.impl that return ClarityFile

Modifier and Type	Method	Description
<E extends LimsEntity<E>> ClarityFile	ClarityAPIImpl.uploadFile(LimsEntityLinkable<E> entity, URL fileURL, boolean publishInLablink)	Attach a file to an entity and upload that file to the file store.

Methods in org.cruk.clarity.api.impl with parameters of type ClarityFile

Modifier and Type	Method	Description
protected void	ClarityAPIImpl.uploadViaHTTP(URLInputStreamResource fileURLResource, ClarityFile targetFile)	Upload a file to the Clarity file store.
protected void	ClarityAPIImpl.uploadViaSFTP(URLInputStreamResource fileURLResource, ClarityFile targetFile)	Upload a file to the Clarity file store.

Method parameters in org.cruk.clarity.api.impl with type arguments of type ClarityFile

Modifier and Type	Method	Description
void	ClarityAPIImpl.deleteAndRemoveFile(Linkable<ClarityFile> file)	Delete a file from the file store and remove its record from the LIMS.
void	ClarityAPIImpl.downloadFile(Linkable<ClarityFile> file, OutputStream resultStream)	Download the given file from its source.