Package ca.corefacility.bioinformatics.irida.service

Interface ProjectService

All Superinterfaces:

CRUDService<java.lang.Long,Project>

All Known Implementing Classes:

ProjectServiceImpl

public interface ProjectService
extends CRUDService<java.lang.Long,Project>

A specialized service layer for projects.

Method Summary

Modifier and Type	Method	Description
Join<Project,ReferenceFile>	addReferenceFileToProject(Project project, ReferenceFile referenceFile)	Add a ReferenceFile to a Project.
RelatedProjectJoin	addRelatedProject(Project subject, Project relatedProject)	Add a related Project to the given Project
Join<Project,Sample>	addSampleToProject(Project project, Sample sample, boolean owner)	Add the specified Sample to the Project.
Join<Project,UserGroup>	addUserGroupToProject(Project project, UserGroup userGroup, ProjectRole role, ProjectMetadataRole metadataRole)	Add the specified UserGroup to the Project with a Role .
Join<Project,User>	addUserToProject(Project project, User user, ProjectRole role, ProjectMetadataRole metadataRole)	Add the specified User to the Project with a Role .
Project	createProjectWithSamples(Project project, java.util.List<java.lang.Long> sampleIds, boolean owner)	Create a Project with the given Samples contained
org.springframework.data.domain.Page<Project>	findAllProjects(java.lang.String searchValue, int currentPage, int length, org.springframework.data.domain.Sort sort)	Find a paged list of all projects (for admin) using the specified search criteria.
org.springframework.data.domain.Page<Project>	findProjectsForUser(java.lang.String search, java.lang.Integer page, java.lang.Integer count, org.springframework.data.domain.Sort sort)	Find a list of projects (for a user or admin) using the specified search criteria
java.lang.Long	getProjectsCreated(java.util.Date createdDate)	Get count of projects created in the time period
java.util.List<GenericStatModel>	getProjectsCreatedGrouped(java.util.Date createdDate, StatisticTimePeriod statisticTimePeriod)	Get list of GenericStatModel of projects created in the past n time period and grouped by the format provided.
java.util.List<ProjectAnalysisSubmissionJoin>	getProjectsForAnalysisSubmission(AnalysisSubmission submission)	Get all Projects a given AnalysisSubmission is shared with
java.util.List<Join<Project,Sample>>	getProjectsForSample(Sample sample)	Get the projects that a given sample is on
java.util.Set<Project>	getProjectsForSequencingObjects(java.util.Collection<? extends SequencingObject> sequences)	Get a Set of all Projects referred to by a collection of SequencingObjects
java.util.List<Join<Project,User>>	getProjectsForUser(User user)	Get all Projects associated with a particular User.
java.util.List<Project>	getProjectsForUserUnique(User user)	Get all Projects associated with a particular User.
java.util.List<Project>	getProjectsUsedInAnalysisSubmission(AnalysisSubmission submission)	Get all Projects that have data used within an AnalysisSubmission.
java.util.List<Project>	getProjectsWithRemoteSyncStatus(RemoteStatus.SyncStatus syncStatus)	Get a list of Projects from remote sites that have a given RemoteStatus.SyncStatus
ProjectUserJoin	getProjectUserJoin(User user, Project project)	Get the ProjectRole of a User on a given Project
java.util.List<RelatedProjectJoin>	getRelatedProjects(Project project)	Get all RelatedProjectJoins for a given Project
java.util.List<Project>	getRemoteProjects()	Get a list of all Projects from remote sites
java.util.List<RelatedProjectJoin>	getReverseRelatedProjects(Project project)	Get all RelatedProjectJoins where the given Project is the relatedProject property.
org.springframework.data.domain.Page<Project>	getUnassociatedProjects(Project p, java.lang.String searchName, java.lang.Integer page, java.lang.Integer count, org.springframework.data.domain.Sort.Direction sortDirection, java.lang.String... sortedBy)	Get a page of projects eligible to be marked as associated projects for the specified project.
java.util.Collection<UserGroupProjectJoin>	getUserGroupProjectJoins(User user, Project project)	Get a collection of UserGroupProjectJoins of a User on a given Project
ProjectSampleJoin	moveSampleBetweenProjects(Project source, Project destination, Sample sample)	Move a Sample from one Project to another
java.util.List<ProjectSampleJoin>	moveSamples(Project source, Project destination, java.util.Collection<Sample> samples)	Move a list of Samples between 2 Project
void	removeReferenceFileFromProject(Project project, ReferenceFile referenceFile)	Remove a ReferenceFile from a Project
void	removeRelatedProject(RelatedProjectJoin relatedProject)	Remove a RelatedProjectJoin
void	removeRelatedProject(Project subject, Project relatedProject)	Remove a RelatedProjectJoin for the given project and related project
void	removeSampleFromProject(Project project, Sample sample)	Remove the specified Sample from the Project.
void	removeSamplesFromProject(Project project, java.lang.Iterable<Sample> samples)	Remove a collection of Samples from a Project
void	removeUserFromProject(Project project, User user)	Remove the specified User from the Project.
void	removeUserGroupFromProject(Project project, UserGroup userGroup)	Remove the specified UserGroup from the Project.
java.util.List<ProjectSampleJoin>	shareSamples(Project source, Project destination, java.util.Collection<Sample> samples, boolean giveOwner)	Share a list of Samples between two Projects.
Project	updateProjectSettings(Project project, java.util.Map<java.lang.String,java.lang.Object> updates)	Update select Project settings
Join<Project,UserGroup>	updateUserGroupProjectMetadataRole(Project project, UserGroup userGroup, ProjectMetadataRole metadataRole)	Update a UserGroup's ProjectMetadataRole on a Project
Join<Project,UserGroup>	updateUserGroupProjectRole(Project project, UserGroup userGroup, ProjectRole projectRole, ProjectMetadataRole metadataRole)	Update a UserGroup's ProjectRole on a Project
Join<Project,User>	updateUserProjectMetadataRole(Project project, User user, ProjectMetadataRole metadataRole)	Update a User's ProjectMetadataRole on a Project
Join<Project,User>	updateUserProjectRole(Project project, User user, ProjectRole projectRole, ProjectMetadataRole metadataRole)	Update a User's ProjectRole on a Project
boolean	userHasProjectRole(User user, Project project, ProjectRole projectRole)	Check if a User has a given ProjectRole on a Project

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

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

Method Detail

addUserToProject

Join<Project,User> addUserToProject(Project project,
                                          User user,
                                          ProjectRole role,
                                          ProjectMetadataRole metadataRole)

Add the specified User to the Project with a Role . If the User is a manager for the Project, then the User should be added to the Project with the 'ROLE_MANAGER' Role.

Parameters:

project - the Project to add the user to.

user - the user to add to the Project.

role - the role that the user plays on the Project.

metadataRole - the access level the user has on the metadata in the project

Returns:

a reference to the relationship resource created between the two entities.

addUserGroupToProject

Join<Project,UserGroup> addUserGroupToProject(Project project,
                                                    UserGroup userGroup,
                                                    ProjectRole role,
                                                    ProjectMetadataRole metadataRole)

Add the specified UserGroup to the Project with a Role . If the UserGroup is a manager for the Project, then the UserGroup should be added to the Project with the 'ROLE_MANAGER' Role.

Parameters:

project - the Project to add the user to.

userGroup - the user group to add to the Project.

role - the role that the group has on the Project.

metadataRole - the ProjectMetadataRole to set for the group

Returns:

a reference to the relationship resource created between the two entities.

removeUserFromProject

void removeUserFromProject(Project project,
                           User user)
                    throws ProjectWithoutOwnerException

Remove the specified User from the Project.

Parameters:

project - the Project to remove the User from.

user - the User to be removed from the Project.

Throws:

ProjectWithoutOwnerException - if removing this user would leave the project without an owner

removeUserGroupFromProject

void removeUserGroupFromProject(Project project,
                                UserGroup userGroup)
                         throws ProjectWithoutOwnerException

Remove the specified UserGroup from the Project.

Parameters:

project - the Project to remove the User from.

userGroup - the UserGroup to be removed from the Project.

Throws:

ProjectWithoutOwnerException - If removing this group leaves the project without an owner

updateUserProjectRole

Join<Project,User> updateUserProjectRole(Project project,
                                               User user,
                                               ProjectRole projectRole,
                                               ProjectMetadataRole metadataRole)
                                        throws ProjectWithoutOwnerException

Update a User's ProjectRole on a Project

Parameters:

project - The project to update

user - The user to update

projectRole - The role to set

metadataRole - ProjectMetadataRole to set for the user

Returns:

The newly updated role object

Throws:

ProjectWithoutOwnerException - If the role change would leave the project without an owner

updateUserProjectMetadataRole

Join<Project,User> updateUserProjectMetadataRole(Project project,
                                                       User user,
                                                       ProjectMetadataRole metadataRole)

Update a User's ProjectMetadataRole on a Project

Parameters:

project - The project to update

user - The user to update

metadataRole - the ProjectMetadataRole to set for the user

Returns:

The newly updated role object

updateUserGroupProjectRole

Join<Project,UserGroup> updateUserGroupProjectRole(Project project,
                                                         UserGroup userGroup,
                                                         ProjectRole projectRole,
                                                         ProjectMetadataRole metadataRole)
                                                  throws ProjectWithoutOwnerException

Update a UserGroup's ProjectRole on a Project

Parameters:

project - The project to update

userGroup - The user group to update

projectRole - The role to set

metadataRole - the ProjectMetadataRole to set for the group

Returns:

The newly updated role object

Throws:

ProjectWithoutOwnerException - If updating the user group leaves the project without an owner

updateUserGroupProjectMetadataRole

Join<Project,UserGroup> updateUserGroupProjectMetadataRole(Project project,
                                                                 UserGroup userGroup,
                                                                 ProjectMetadataRole metadataRole)

Update a UserGroup's ProjectMetadataRole on a Project

Parameters:

project - The project to update

userGroup - The user group to update

metadataRole - the ProjectMetadataRole to set for the group

Returns:

The newly updated role object

addSampleToProject

Join<Project,Sample> addSampleToProject(Project project,
                                              Sample sample,
                                              boolean owner)

Add the specified Sample to the Project.

Parameters:

project - the Project to add the Sample to.

sample - the Sample to add to the Project. If the Sample has not previously been persisted, the service will persist the Sample.

owner - Whether the project will have modification access for this sample

Returns:

a reference to the relationship resource created between the two entities.

moveSampleBetweenProjects

ProjectSampleJoin moveSampleBetweenProjects(Project source,
                                            Project destination,
                                            Sample sample)

Move a Sample from one Project to another

Parameters:

source - the source Project

destination - Destination Project

sample - The sample to move

Returns:

Newly created ProjectSampleJoin

shareSamples

java.util.List<ProjectSampleJoin> shareSamples(Project source,
                                               Project destination,
                                               java.util.Collection<Sample> samples,
                                               boolean giveOwner)

Share a list of Samples between two Projects.

Parameters:

source - the source Project

destination - the Project being shared into

samples - a collection of Sample

giveOwner - whether to give ownership rights to the destination Project

Returns:

a list of new ProjectSampleJoin

moveSamples

java.util.List<ProjectSampleJoin> moveSamples(Project source,
                                              Project destination,
                                              java.util.Collection<Sample> samples)

Move a list of Samples between 2 Project

Parameters:

source - the source Project

destination - the Project being moved to

samples - a collection of Samples Project

Returns:

a list of new ProjectSampleJoin

removeSampleFromProject

void removeSampleFromProject(Project project,
                             Sample sample)

Remove the specified Sample from the Project. The Sample will also be deleted from the system because Samples cannot exist outside of a Project.

Parameters:

project - the Project to remove the Sample from.

sample - the Sample to remove.

removeSamplesFromProject

void removeSamplesFromProject(Project project,
                              java.lang.Iterable<Sample> samples)

Remove a collection of Samples from a Project

Parameters:

project - the Project to remove the Samples from.

samples - the Samples to remove.

getProjectsForUser

java.util.List<Join<Project,User>> getProjectsForUser(User user)

Get all Projects associated with a particular User.

Parameters:

user - the user to get projects for.

Returns:

the projects associated with the user.

getProjectsForUserUnique

java.util.List<Project> getProjectsForUserUnique(User user)

Get all Projects associated with a particular User.

Parameters:

user - the user to get the unique projects for.

Returns:

the projects associated with the user.

userHasProjectRole

boolean userHasProjectRole(User user,
                           Project project,
                           ProjectRole projectRole)

Check if a User has a given ProjectRole on a Project

Parameters:

user - The user to test

project - The project to test

projectRole - The project role to test

Returns:

true/false whether the user has the given role

getProjectUserJoin

ProjectUserJoin getProjectUserJoin(User user,
                                   Project project)

Get the ProjectRole of a User on a given Project

Parameters:

user - The user

project - The project

Returns:

the ProjectRole of the user on the project

getUserGroupProjectJoins

java.util.Collection<UserGroupProjectJoin> getUserGroupProjectJoins(User user,
                                                                    Project project)

Get a collection of UserGroupProjectJoins of a User on a given Project

Parameters:

user - The user

project - The project

Returns:

the collection of UserGroupProjectJoins of the user on the project

addRelatedProject

RelatedProjectJoin addRelatedProject(Project subject,
                                     Project relatedProject)

Add a related Project to the given Project

Parameters:

subject - The parent project

relatedProject - The project to be added to the parent

Returns:

a RelatedProjectJoin describing the relationship

getRelatedProjects

java.util.List<RelatedProjectJoin> getRelatedProjects(Project project)

Get all RelatedProjectJoins for a given Project

Parameters:

project - The parent project

Returns:

A list of RelatedProjectJoin

getReverseRelatedProjects

java.util.List<RelatedProjectJoin> getReverseRelatedProjects(Project project)

Get all RelatedProjectJoins where the given Project is the relatedProject property.

Parameters:

project - The child project

Returns:

A list of RelatedProjectJoin

removeRelatedProject

void removeRelatedProject(RelatedProjectJoin relatedProject)

Remove a RelatedProjectJoin

Parameters:

relatedProject - The RelatedProjectJoin to remove

removeRelatedProject

void removeRelatedProject(Project subject,
                          Project relatedProject)

Remove a RelatedProjectJoin for the given project and related project

Parameters:

subject - the owning project

relatedProject - The related project

getProjectsForSample

java.util.List<Join<Project,Sample>> getProjectsForSample(Sample sample)

Get the projects that a given sample is on

Parameters:

sample - The sample to get projects for

Returns:

All the projects a sample exists in

addReferenceFileToProject

Join<Project,ReferenceFile> addReferenceFileToProject(Project project,
                                                            ReferenceFile referenceFile)

Add a ReferenceFile to a Project.

Parameters:

project - the Project to add the ReferenceFile to.

referenceFile - the ReferenceFile.

Returns:

a Join representing the relationship between the Project and ReferenceFile.

removeReferenceFileFromProject

void removeReferenceFileFromProject(Project project,
                                    ReferenceFile referenceFile)

Remove a ReferenceFile from a Project

Parameters:

project - the Project to remove the reference file from.

referenceFile - the ReferenceFile to remove.

getUnassociatedProjects

org.springframework.data.domain.Page<Project> getUnassociatedProjects(Project p,
                                                                      java.lang.String searchName,
                                                                      java.lang.Integer page,
                                                                      java.lang.Integer count,
                                                                      org.springframework.data.domain.Sort.Direction sortDirection,
                                                                      java.lang.String... sortedBy)

Get a page of projects eligible to be marked as associated projects for the specified project.

Parameters:

p - the project to get eligible associated projects.

searchName - the name of projects to filter on.

page - the requested page of results.

count - the number of results on the page.

sortDirection - the direction the results should be sorted by.

sortedBy - the property to be used to sort the results.

Returns:

a page of projects eligible to be marked as associated projects.

findProjectsForUser

org.springframework.data.domain.Page<Project> findProjectsForUser(java.lang.String search,
                                                                  java.lang.Integer page,
                                                                  java.lang.Integer count,
                                                                  org.springframework.data.domain.Sort sort)

Find a list of projects (for a user or admin) using the specified search criteria

Parameters:

search - String generic string to search terms for

page - Integer current page viewed.

count - Integer length of current page.

sort - Sort Current table sort properties.

Returns:

Page of Project

findAllProjects

org.springframework.data.domain.Page<Project> findAllProjects(java.lang.String searchValue,
                                                              int currentPage,
                                                              int length,
                                                              org.springframework.data.domain.Sort sort)

Find a paged list of all projects (for admin) using the specified search criteria.

Parameters:

searchValue - String generic string to search terms for

currentPage - Integer current page viewed.

length - Integer length of current page.

sort - Sort Current table sort properties.

Returns:

Page of Project

getProjectsWithRemoteSyncStatus

java.util.List<Project> getProjectsWithRemoteSyncStatus(RemoteStatus.SyncStatus syncStatus)

Get a list of Projects from remote sites that have a given RemoteStatus.SyncStatus

Parameters:

syncStatus - the RemoteStatus.SyncStatus to get Projects for

Returns:

a list of Project

getRemoteProjects

java.util.List<Project> getRemoteProjects()

Get a list of all Projects from remote sites

Returns:

a list of Project

getProjectsForSequencingObjects

java.util.Set<Project> getProjectsForSequencingObjects(java.util.Collection<? extends SequencingObject> sequences)

Get a Set of all Projects referred to by a collection of SequencingObjects

Parameters:

sequences - the SequencingObjects to get Projects for

Returns:

a set of Project

getProjectsForAnalysisSubmission

java.util.List<ProjectAnalysisSubmissionJoin> getProjectsForAnalysisSubmission(AnalysisSubmission submission)

Get all Projects a given AnalysisSubmission is shared with

Parameters:

submission - the AnalysisSubmission

Returns:

a list of ProjectAnalysisSubmissionJoins

getProjectsUsedInAnalysisSubmission

java.util.List<Project> getProjectsUsedInAnalysisSubmission(AnalysisSubmission submission)

Get all Projects that have data used within an AnalysisSubmission. Note that this differs from getProjectsForAnalysisSubmission(AnalysisSubmission) where that method only returns projects which the AnalysisSubmission is explicitly shared with.

Parameters:

submission - the AnalysisSubmission to get Projects for

Returns:

a list of Projects

updateProjectSettings

Project updateProjectSettings(Project project,
                              java.util.Map<java.lang.String,java.lang.Object> updates)

Update select Project settings

Parameters:

project - the project to update

updates - a map of fields to update

Returns:

the updated Project

createProjectWithSamples

Project createProjectWithSamples(Project project,
                                 java.util.List<java.lang.Long> sampleIds,
                                 boolean owner)

Create a Project with the given Samples contained

Parameters:

project - the Project to create

sampleIds - IDs of the Samples

owner - whether to lock Sample modification from new project

Returns:

the created Project

getProjectsCreated

java.lang.Long getProjectsCreated(java.util.Date createdDate)

Get count of projects created in the time period

Parameters:

createdDate - the minimum date for projects created

Returns:

An Long count of projects created

getProjectsCreatedGrouped

java.util.List<GenericStatModel> getProjectsCreatedGrouped(java.util.Date createdDate,
                                                           StatisticTimePeriod statisticTimePeriod)

Get list of GenericStatModel of projects created in the past n time period and grouped by the format provided.

Parameters:

createdDate - the minimum date for projects created

statisticTimePeriod - the enum containing format for which to group the results by

Returns:

An GenericStatModel list