Package ca.corefacility.bioinformatics.irida.service.impl.sample

Class MetadataTemplateServiceImpl

java.lang.Object

ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl<java.lang.Long,MetadataTemplate>

ca.corefacility.bioinformatics.irida.service.impl.sample.MetadataTemplateServiceImpl

All Implemented Interfaces:

CRUDService<java.lang.Long,MetadataTemplate>, MetadataTemplateService

@Service
public class MetadataTemplateServiceImpl
extends CRUDServiceImpl<java.lang.Long,MetadataTemplate>
implements MetadataTemplateService

Service for storing and reading MetadataTemplates

Field Summary

Fields inherited from class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

CREATED_DATE_SORT_PROPERTY, repository, validator, valueType

Constructor Summary

Constructors

Constructor	Description
MetadataTemplateServiceImpl(MetadataTemplateRepository repository, MetadataFieldRepository fieldRepository, javax.validation.Validator validator, MetadataRestrictionRepository metadataRestrictionRepository, UserRepository userRepository, ProjectUserJoinRepository pujRepository, UserGroupProjectJoinRepository userGroupProjectJoinRepository)

Method Summary

Modifier and Type	Method	Description
java.util.Set<MetadataEntry>	convertMetadataStringsToSet(java.util.Map<java.lang.String,MetadataEntry> metadataMap)	Get the appropriate MetadataTemplateFields and MetadataEntrys for a given map of Strings
MetadataTemplate	createMetadataTemplateInProject(MetadataTemplate template, Project project)	Create a new MetadataTemplate for a Project
void	deleteMetadataTemplateFromProject(Project project, java.lang.Long id)	Deleta a MetadataTemplate from a Project
java.util.List<MetadataTemplateField>	getAllMetadataFieldsByQueryString(java.lang.String query)	Get a list of all MetadataTemplateFields that contain the query
MetadataTemplate	getDefaultTemplateForProject(Project project)	Get the default MetadataTemplate for the given Project (if one exists)
java.util.List<MetadataTemplateField>	getMetadataFieldsForProject(Project project)	Get all the MetadataTemplateFields on a given Project
MetadataRestriction	getMetadataRestrictionForFieldAndProject(Project project, MetadataTemplateField field)	Get the MetadataRestriction for the given MetadataTemplateField and Project
java.util.List<MetadataRestriction>	getMetadataRestrictionsForProject(Project project)	List all the MetadataRestriction for the given Project
java.util.List<MetadataTemplate>	getMetadataTemplatesForProject(Project project)	Get a list of MetadataTemplates for a given Project
java.util.List<MetadataTemplateField>	getPermittedFieldsForCurrentUser(Project project, boolean includeTemplateFields)	Get all MetadataTemplateField that the currently logged in user is allowed to read
java.util.List<MetadataTemplateField>	getPermittedFieldsForTemplate(MetadataTemplate template)	Get all MetadataTemplateField the current user is allowed to read for a MetadataTemplate
java.util.List<StaticMetadataTemplateField>	getStaticMetadataFields()	Get a list of all StaticMetadataTemplateFields available
MetadataTemplate	read(java.lang.Long id)	Read the object type by unique identifier.
MetadataTemplateField	readMetadataField(java.lang.Long id)	Get a MetadataTemplateField by its Long identifier
MetadataTemplateField	readMetadataFieldByKey(java.lang.String key)	Read a MetadataTemplateField by its key
MetadataTemplateField	readMetadataFieldByLabel(java.lang.String label)	Get a MetadataTemplateField by its String label
void	removeDefaultMetadataTemplateForProject(Project project)	Remove the default MetadataTemplate from the project.
MetadataTemplateField	saveMetadataField(MetadataTemplateField field)	Save a new metadata fields
MetadataRestriction	setMetadataRestriction(Project project, MetadataTemplateField field, ProjectMetadataRole role)	Adds or updates the MetadataRestriction for a project and field
MetadataTemplate	updateDefaultMetadataTemplateForProject(Project project, MetadataTemplate template)	Update which MetadataTemplate is the default for the given Project
MetadataTemplate	updateMetadataTemplateInProject(MetadataTemplate template)	Update a MetadataTemplate within a Project

Methods inherited from class ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl

count, create, delete, exists, findAll, findRevisions, findRevisions, list, list, list, readMultiple, search, search, update, updateFields, updateMultiple

Methods inherited from class java.lang.Object

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

Methods inherited from interface ca.corefacility.bioinformatics.irida.service.CRUDService

count, create, delete, exists, findAll, findRevisions, findRevisions, list, list, list, readMultiple, search, search, update, updateFields, updateMultiple

Constructor Detail

MetadataTemplateServiceImpl

@Autowired
public MetadataTemplateServiceImpl(MetadataTemplateRepository repository,
                                   MetadataFieldRepository fieldRepository,
                                   javax.validation.Validator validator,
                                   MetadataRestrictionRepository metadataRestrictionRepository,
                                   UserRepository userRepository,
                                   ProjectUserJoinRepository pujRepository,
                                   UserGroupProjectJoinRepository userGroupProjectJoinRepository)

Method Detail

read

@PreAuthorize("hasPermission(#id, \'canReadMetadataTemplate\')")
public MetadataTemplate read(java.lang.Long id)
                      throws EntityNotFoundException

Read the object type by unique identifier.

Specified by:

read in interface CRUDService<java.lang.Long,MetadataTemplate>

Overrides:

read in class CRUDServiceImpl<java.lang.Long,MetadataTemplate>

Parameters:

id - The unique identifier for this object.

Returns:

The object corresponding to the unique identifier.

Throws:

EntityNotFoundException - If the identifier does not exist in the database.

updateMetadataTemplateInProject

@PreAuthorize("hasPermission(#template, \'canUpdateMetadataTemplate\')")
public MetadataTemplate updateMetadataTemplateInProject(MetadataTemplate template)

Update a MetadataTemplate within a Project

Specified by:

updateMetadataTemplateInProject in interface MetadataTemplateService

Parameters:

template - MetadataTemplate

Returns:

MetadataTemplate

deleteMetadataTemplateFromProject

@PreAuthorize("hasPermission(#id, \'canUpdateMetadataTemplate\')")
public void deleteMetadataTemplateFromProject(Project project,
                                              java.lang.Long id)
                                       throws EntityNotFoundException

Deleta a MetadataTemplate from a Project

Specified by:

deleteMetadataTemplateFromProject in interface MetadataTemplateService

Parameters:

project - the Project to template lives in.

id - the Long identifier for a MetadataTemplate

Throws:

EntityNotFoundException

createMetadataTemplateInProject

@PreAuthorize("hasPermission(#project, \'isProjectOwner\')")
public MetadataTemplate createMetadataTemplateInProject(MetadataTemplate template,
                                                        Project project)

Create a new MetadataTemplate for a Project

Specified by:

createMetadataTemplateInProject in interface MetadataTemplateService

Parameters:

template - the MetadataTemplate to create

project - the Project to create the template in

Returns:

a MetadataTemplate

getMetadataTemplatesForProject

@PreAuthorize("hasPermission(#project, \'canReadProject\')")
public java.util.List<MetadataTemplate> getMetadataTemplatesForProject(Project project)

Get a list of MetadataTemplates for a given Project

Specified by:

getMetadataTemplatesForProject in interface MetadataTemplateService

Parameters:

project - the Project

Returns:

a list of MetadataTemplate

readMetadataField

@PreAuthorize("permitAll()")
public MetadataTemplateField readMetadataField(java.lang.Long id)

Description copied from interface: MetadataTemplateService

Get a MetadataTemplateField by its Long identifier

Specified by:

readMetadataField in interface MetadataTemplateService

Parameters:

id - Long identifier for a MetadataTemplateField

Returns:

MetadataTemplateField

readMetadataFieldByLabel

@PreAuthorize("permitAll()")
public MetadataTemplateField readMetadataFieldByLabel(java.lang.String label)

Get a MetadataTemplateField by its String label

Specified by:

readMetadataFieldByLabel in interface MetadataTemplateService

Parameters:

label - the String label for the MetadataTemplateField.

Returns:

MetadataTemplateField

readMetadataFieldByKey

@PreAuthorize("permitAll()")
public MetadataTemplateField readMetadataFieldByKey(java.lang.String key)

Description copied from interface: MetadataTemplateService

Read a MetadataTemplateField by its key

Specified by:

readMetadataFieldByKey in interface MetadataTemplateService

Parameters:

key - key for the field

Returns:

a MetadataTemplateField

getStaticMetadataFields

@PreAuthorize("permitAll()")
public java.util.List<StaticMetadataTemplateField> getStaticMetadataFields()

Description copied from interface: MetadataTemplateService

Get a list of all StaticMetadataTemplateFields available

Specified by:

getStaticMetadataFields in interface MetadataTemplateService

Returns:

a list of StaticMetadataTemplateField

saveMetadataField

@PreAuthorize("permitAll()")
public MetadataTemplateField saveMetadataField(MetadataTemplateField field)

Description copied from interface: MetadataTemplateService

Save a new metadata fields

Specified by:

saveMetadataField in interface MetadataTemplateService

Parameters:

field - the MetadataTemplateField to save.

Returns:

the saved MetadataTemplateField

getAllMetadataFieldsByQueryString

@PreAuthorize("permitAll()")
public java.util.List<MetadataTemplateField> getAllMetadataFieldsByQueryString(java.lang.String query)

Get a list of all MetadataTemplateFields that contain the query

Specified by:

getAllMetadataFieldsByQueryString in interface MetadataTemplateService

Parameters:

query - the String to search labels for.

Returns:

List of MetadataTemplateField

convertMetadataStringsToSet

@PreAuthorize("permitAll()")
public java.util.Set<MetadataEntry> convertMetadataStringsToSet(java.util.Map<java.lang.String,MetadataEntry> metadataMap)

Get the appropriate MetadataTemplateFields and MetadataEntrys for a given map of Strings

Specified by:

convertMetadataStringsToSet in interface MetadataTemplateService

Parameters:

metadataMap - the strings to convert

Returns:

a Set of MetadataEntrys

getMetadataFieldsForProject

@PreAuthorize("hasPermission(#project, \'canReadProject\')")
public java.util.List<MetadataTemplateField> getMetadataFieldsForProject(Project project)

Get all the MetadataTemplateFields on a given Project

Specified by:

getMetadataFieldsForProject in interface MetadataTemplateService

Parameters:

project - the Project to get fields for

Returns:

a list of fields

getMetadataRestrictionForFieldAndProject

@PreAuthorize("hasPermission(#project, \'canReadProject\')")
public MetadataRestriction getMetadataRestrictionForFieldAndProject(Project project,
                                                                    MetadataTemplateField field)

Description copied from interface: MetadataTemplateService

Get the MetadataRestriction for the given MetadataTemplateField and Project

Specified by:

getMetadataRestrictionForFieldAndProject in interface MetadataTemplateService

Parameters:

project - the Project to get the restriction for

field - the MetadataTemplateField to get the restriction for

Returns:

The found MetadataRestriction. If there is no restriction defined, this may be null

getMetadataRestrictionsForProject

@PreAuthorize("hasPermission(#project, \'canReadProject\')")
public java.util.List<MetadataRestriction> getMetadataRestrictionsForProject(Project project)

Description copied from interface: MetadataTemplateService

List all the MetadataRestriction for the given Project

Specified by:

getMetadataRestrictionsForProject in interface MetadataTemplateService

Parameters:

project - the Project the Project to get restrictions for

Returns:

a List of all defined MetadataRestriction

setMetadataRestriction

@PreAuthorize("hasPermission(#project, \'isProjectOwner\')")
public MetadataRestriction setMetadataRestriction(Project project,
                                                  MetadataTemplateField field,
                                                  ProjectMetadataRole role)

Description copied from interface: MetadataTemplateService

Adds or updates the MetadataRestriction for a project and field

Specified by:

setMetadataRestriction in interface MetadataTemplateService

Parameters:

project - the Project to add a restriction for

field - the field to set a restriction on

role - the role level to set the restriction for

Returns:

the created MetadataRestriction

getPermittedFieldsForTemplate

@PreAuthorize("hasPermission(#template, \'canReadMetadataTemplate\')")
public java.util.List<MetadataTemplateField> getPermittedFieldsForTemplate(MetadataTemplate template)

Get all MetadataTemplateField the current user is allowed to read for a MetadataTemplate

Specified by:

getPermittedFieldsForTemplate in interface MetadataTemplateService

Parameters:

template - the MetadataTemplate to get fields for

Returns:

a list of MetadataTemplateField

getPermittedFieldsForCurrentUser

@PreAuthorize("hasPermission(#project, \'canReadProject\')")
public java.util.List<MetadataTemplateField> getPermittedFieldsForCurrentUser(Project project,
                                                                              boolean includeTemplateFields)

Get all MetadataTemplateField that the currently logged in user is allowed to read

Specified by:

getPermittedFieldsForCurrentUser in interface MetadataTemplateService

Parameters:

project - the Project to request fields from

includeTemplateFields - whether to include fields from the project's associated MetadataTemplates

Returns:

a list of MetadataTemplateField collecting the allowed MetadataTemplateField

getDefaultTemplateForProject

@PreAuthorize("hasPermission(#project, \'canReadProject\')")
public MetadataTemplate getDefaultTemplateForProject(Project project)

Get the default MetadataTemplate for the given Project (if one exists)

Specified by:

getDefaultTemplateForProject in interface MetadataTemplateService

Parameters:

project - the Project to get the template for

Returns:

the default MetadataTemplate if one is set

updateDefaultMetadataTemplateForProject

@PreAuthorize("hasPermission(#project, \'canManageLocalProjectSettings\')")
public MetadataTemplate updateDefaultMetadataTemplateForProject(Project project,
                                                                MetadataTemplate template)

Update which MetadataTemplate is the default for the given Project

Specified by:

updateDefaultMetadataTemplateForProject in interface MetadataTemplateService

Parameters:

project - the Project to set a template on

template - the MetadataTemplate to set

Returns:

the new default MetadataTemplate

removeDefaultMetadataTemplateForProject

@PreAuthorize("hasPermission(#project, \'canManageLocalProjectSettings\')")
public void removeDefaultMetadataTemplateForProject(Project project)

Remove the default MetadataTemplate from the project. It will now use all fields as default

Specified by:

removeDefaultMetadataTemplateForProject in interface MetadataTemplateService

Parameters:

project - the Project to remove the template from