A C D E F G I L M N O P R S U V W 

A

addParticipant(Integer, Integer, List<Integer>) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Add specified Participant to Project with specified roles Roles must be roles of project
addParticipant(Integer, Integer, List<Integer>) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
addParticipant(Integer, Integer) - Method in interface org.galaxy.service.workgroupmanagement.IWorkgroupManagement
Add specified Participant to specified Workgroup
addParticipant(Integer, Integer) - Method in class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
addParticipants(Integer, List<Integer>, List<Integer>) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Add specified participant to Project
addParticipants(Integer, List<Integer>, List<Integer>) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
addParticipants(Integer, List<Integer>) - Method in interface org.galaxy.service.workgroupmanagement.IWorkgroupManagement
Add specified Participants to specified Workgroup
addParticipants(Integer, List<Integer>) - Method in class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
address - Variable in class org.galaxy.model.EParticipant
 
address - Variable in class org.galaxy.service.usermanagement.Participant
 
addRole(Integer, Integer) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Add specified Role to specified Project
addRole(Integer, Integer) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
addRoles(Integer, List<Integer>) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Add specified roles to Project
addRoles(Integer, List<Integer>) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
analyser - Variable in class org.galaxy.service.modelfragment.ModelFragmentManagement
 

C

calculateDependency(EModelFragment) - Method in class org.galaxy.service.modelfragment.ModelFragmentManagement
 
calculateImpacte(EModelFragment) - Method in class org.galaxy.service.modelfragment.ModelFragmentManagement
 
calculateLocalPath(String, String) - Method in class org.galaxy.utility.filerepository.FileRepository
 
calculateLocalPath(String, String) - Method in interface org.galaxy.utility.filerepository.IFileRepository
Calculates the path of the file on the repository from its name and version
category - Variable in class org.galaxy.model.ERole
 
category - Variable in class org.galaxy.service.rolemanagement.Role
 
copy(File, File) - Method in class org.galaxy.utility.filerepository.FileRepository
 
country - Variable in class org.galaxy.model.EParticipant
 
country - Variable in class org.galaxy.service.usermanagement.Participant
 
createParticipant(Participant) - Method in interface org.galaxy.service.usermanagement.IUserManagement
Creates a new participant with the given name.
createParticipant(Participant) - Method in class org.galaxy.service.usermanagement.UserManagement
 
createProject(Project) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Creates a new project in the system .It returns the id of project
createProject(Project) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
createRole(Role) - Method in interface org.galaxy.service.rolemanagement.IRoleManagement
Creates a new role in the system .It returns the id of role
createRole(Role) - Method in class org.galaxy.service.rolemanagement.RoleManagement
 
createWorkgroup(Workgroup) - Method in interface org.galaxy.service.workgroupmanagement.IWorkgroupManagement
Creates a new group in the system.
createWorkgroup(Workgroup) - Method in class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
ctx - Variable in class org.galaxy.service.modelfragment.ModelFragmentManagement
 

D

deleteFile(String, String) - Method in class org.galaxy.utility.filerepository.FileRepository
 
deleteFile(String, String) - Method in interface org.galaxy.utility.filerepository.IFileRepository
Deleting a file contained in Model Fragments repository
deleteModelFragment(String, String) - Method in interface org.galaxy.service.modelfragment.IModelFragmentManagement
Deletes the given ModelFragment from the system
deleteModelFragment(String, String) - Method in class org.galaxy.service.modelfragment.ModelFragmentManagement
 
deleteModelFragments(List<ModelFragmentData>) - Method in interface org.galaxy.service.modelfragment.IModelFragmentManagement
Delete the given ModelFragment from the system
deleteModelFragments(List<ModelFragmentData>) - Method in class org.galaxy.service.modelfragment.ModelFragmentManagement
 
deleteParticipant(Integer) - Method in interface org.galaxy.service.usermanagement.IUserManagement
Delete the given participant from the system
deleteParticipant(Integer) - Method in class org.galaxy.service.usermanagement.UserManagement
 
deleteParticipants(List<Integer>) - Method in interface org.galaxy.service.usermanagement.IUserManagement
Delete the givens participants from the system
deleteParticipants(List<Integer>) - Method in class org.galaxy.service.usermanagement.UserManagement
 
deleteProject(Integer) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Delete the given project from the system
deleteProject(Integer) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
deleteProjects(List<Integer>) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Delete the given projects from the system
deleteProjects(List<Integer>) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
deleteRole(Integer) - Method in interface org.galaxy.service.rolemanagement.IRoleManagement
Delete the given role from the system
deleteRole(Integer) - Method in class org.galaxy.service.rolemanagement.RoleManagement
 
deleteRoles(List<Integer>) - Method in interface org.galaxy.service.rolemanagement.IRoleManagement
Delete the given roles from the system
deleteRoles(List<Integer>) - Method in class org.galaxy.service.rolemanagement.RoleManagement
 
deleteWorkgroup(Integer) - Method in interface org.galaxy.service.workgroupmanagement.IWorkgroupManagement
Deletes the given workgroup from the system
deleteWorkgroup(Integer) - Method in class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
deleteWorkgroups(List<Integer>) - Method in interface org.galaxy.service.workgroupmanagement.IWorkgroupManagement
Delete the given workgroups from the system
deleteWorkgroups(List<Integer>) - Method in class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
dependencies - Variable in class org.galaxy.model.EModelFragment
 
dependencies - Variable in class org.galaxy.service.modelfragment.ModelFragmentData
 
description - Variable in class org.galaxy.model.EModelFragment
 
description - Variable in class org.galaxy.model.EProject
 
description - Variable in class org.galaxy.model.ERole
 
description - Variable in class org.galaxy.model.EWorkgroup
 
description - Variable in class org.galaxy.service.modelfragment.ModelFragmentData
 
description - Variable in class org.galaxy.service.projectmanagement.Project
 
description - Variable in class org.galaxy.service.rolemanagement.Role
 
description - Variable in class org.galaxy.service.workgroupmanagement.Workgroup
 

E

email - Variable in class org.galaxy.model.EParticipant
 
email - Variable in class org.galaxy.service.usermanagement.Participant
 
EModelFragment - Class in org.galaxy.model
Object-relational persistence model dedicated to ModelFragment
EModelFragment() - Constructor for class org.galaxy.model.EModelFragment
 
endDate - Variable in class org.galaxy.model.EProject
 
endDate - Variable in class org.galaxy.service.projectmanagement.Project
 
EParticipant - Class in org.galaxy.model
Object-relational persistence model dedicated to Participant
EParticipant() - Constructor for class org.galaxy.model.EParticipant
 
EProject - Class in org.galaxy.model
Object-relational persistence model dedicated to Project
EProject() - Constructor for class org.galaxy.model.EProject
 
EProjectParticipant - Class in org.galaxy.model
Object-relational persistence model dedicated to Project Participant relation
EProjectParticipant() - Constructor for class org.galaxy.model.EProjectParticipant
 
equals(Object) - Method in class org.galaxy.model.EModelFragment
 
equals(Object) - Method in class org.galaxy.model.EParticipant
 
equals(Object) - Method in class org.galaxy.model.EProject
 
equals(Object) - Method in class org.galaxy.model.ERole
 
equals(Object) - Method in class org.galaxy.model.EWorkgroup
 
equals(Object) - Method in class org.galaxy.service.usermanagement.Participant
 
ERole - Class in org.galaxy.model
Object-relational persistence model dedicated to Project Role
ERole() - Constructor for class org.galaxy.model.ERole
 
EWorkgroup - Class in org.galaxy.model
Object-relational persistence model dedicated to Workgroup
EWorkgroup() - Constructor for class org.galaxy.model.EWorkgroup
 
extractMetadata(File) - Method in class org.galaxy.utility.fragmentanalyser.FragmentAnalyser
 
extractMetadata(File) - Method in interface org.galaxy.utility.fragmentanalyser.IFragmentAnalyser
Metadata extraction from the ModelFragment file

F

FileRepository - Class in org.galaxy.utility.filerepository
Implementation of IFileRepository services dedicated to management of physical ModelFragment repository management
FileRepository() - Constructor for class org.galaxy.utility.filerepository.FileRepository
 
findAllModelFragments() - Method in interface org.galaxy.service.modelfragment.IModelFragmentManagement
Return list of all Model Fragment in Galaxy repository
findAllModelFragments() - Method in class org.galaxy.service.modelfragment.ModelFragmentManagement
 
findAllParticipants() - Method in interface org.galaxy.service.usermanagement.IUserManagement
List all the existing participant.
findAllParticipants() - Method in class org.galaxy.service.usermanagement.UserManagement
 
findAllProjects() - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
List all existing projects.
findAllProjects() - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
findAllRoles() - Method in interface org.galaxy.service.rolemanagement.IRoleManagement
List all existing role.
findAllRoles() - Method in class org.galaxy.service.rolemanagement.RoleManagement
 
findAllWorkgroups() - Method in interface org.galaxy.service.workgroupmanagement.IWorkgroupManagement
List all existing workgroup.
findAllWorkgroups() - Method in class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
findModelFragmentById(String, String) - Method in interface org.galaxy.service.modelfragment.IModelFragmentManagement
Return Model Fragment in Galaxy repository
findModelFragmentById(String, String) - Method in class org.galaxy.service.modelfragment.ModelFragmentManagement
 
findModelFragmentByIds(List<ModelFragmentData>) - Method in interface org.galaxy.service.modelfragment.IModelFragmentManagement
Return List ofModel Fragment in Galaxy repository
findModelFragmentByIds(List<ModelFragmentData>) - Method in class org.galaxy.service.modelfragment.ModelFragmentManagement
 
findModelFragmentsByNameAndVersion(String, String) - Method in interface org.galaxy.service.modelfragment.IModelFragmentManagement
Return a subset of Model Fragment in Galaxy repository The Model Fragment list is filtered based on patterns namePattern and versionPattern
findModelFragmentsByNameAndVersion(String, String) - Method in class org.galaxy.service.modelfragment.ModelFragmentManagement
 
findParticipantById(Integer) - Method in interface org.galaxy.service.usermanagement.IUserManagement
Find a participant identified by his Identifier
findParticipantById(Integer) - Method in class org.galaxy.service.usermanagement.UserManagement
 
findParticipantsByIds(List<Integer>) - Method in interface org.galaxy.service.usermanagement.IUserManagement
Find participants identified by ther Identifier
findParticipantsByIds(List<Integer>) - Method in class org.galaxy.service.usermanagement.UserManagement
 
findParticipantsByProject(Integer) - Method in interface org.galaxy.service.usermanagement.IUserManagement
List all participant of specified project.
findParticipantsByProject(Integer) - Method in class org.galaxy.service.usermanagement.UserManagement
 
findParticipantsByProjectAndRoles(Integer, List<Integer>) - Method in interface org.galaxy.service.usermanagement.IUserManagement
List all participant of specified project whith specified roles.
findParticipantsByProjectAndRoles(Integer, List<Integer>) - Method in class org.galaxy.service.usermanagement.UserManagement
 
findParticipantsByWorkgroup(Integer) - Method in interface org.galaxy.service.usermanagement.IUserManagement
List all participant of specified workgroup.
findParticipantsByWorkgroup(Integer) - Method in class org.galaxy.service.usermanagement.UserManagement
 
findProjectById(Integer) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Find a project identified by his Identifier
findProjectById(Integer) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
findProjectByIds(List<Integer>) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Find a list project identified by her Identifier
findProjectByIds(List<Integer>) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
findProjectsByParticipant(Integer) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
List all project of specified participant.
findProjectsByParticipant(Integer) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
findRoleById(Integer) - Method in interface org.galaxy.service.rolemanagement.IRoleManagement
Find a role identified by his Identifier
findRoleById(Integer) - Method in class org.galaxy.service.rolemanagement.RoleManagement
 
findRoleByIds(List<Integer>) - Method in interface org.galaxy.service.rolemanagement.IRoleManagement
Find List of role identified by her Identifier
findRoleByIds(List<Integer>) - Method in class org.galaxy.service.rolemanagement.RoleManagement
 
findRolesByProject(Integer) - Method in interface org.galaxy.service.rolemanagement.IRoleManagement
List all role of specified project.
findRolesByProject(Integer) - Method in class org.galaxy.service.rolemanagement.RoleManagement
 
findRolesByProjectAndParticipant(Integer, Integer) - Method in interface org.galaxy.service.rolemanagement.IRoleManagement
List all role of participantId in specified project.
findRolesByProjectAndParticipant(Integer, Integer) - Method in class org.galaxy.service.rolemanagement.RoleManagement
 
findWorkgroupById(Integer) - Method in interface org.galaxy.service.workgroupmanagement.IWorkgroupManagement
Find a workgroup identified by his Identifier
findWorkgroupById(Integer) - Method in class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
findWorkgroupsByIds(List<Integer>) - Method in interface org.galaxy.service.workgroupmanagement.IWorkgroupManagement
Find workgroups identified by her identifiers
findWorkgroupsByIds(List<Integer>) - Method in class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
findWorkgroupsByParticipant(Integer) - Method in interface org.galaxy.service.workgroupmanagement.IWorkgroupManagement
List all workgroup of specified participant.
findWorkgroupsByParticipant(Integer) - Method in class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
firstName - Variable in class org.galaxy.model.EParticipant
 
firstName - Variable in class org.galaxy.service.usermanagement.Participant
 
FragmentAnalyser - Class in org.galaxy.utility.fragmentanalyser
Implementation of IFragmentAnalyser services dedicated to ModelFragment manipulation
FragmentAnalyser() - Constructor for class org.galaxy.utility.fragmentanalyser.FragmentAnalyser
 
fragments - Variable in class org.galaxy.model.EWorkgroup
 

G

galaxyId - Variable in class org.galaxy.model.EModelFragment
 
galaxyId - Variable in class org.galaxy.service.modelfragment.ModelFragmentData
 
getAddress() - Method in class org.galaxy.model.EParticipant
 
getAddress() - Method in class org.galaxy.service.usermanagement.Participant
 
getCategory() - Method in class org.galaxy.model.ERole
 
getCategory() - Method in class org.galaxy.service.rolemanagement.Role
 
getCountry() - Method in class org.galaxy.model.EParticipant
 
getCountry() - Method in class org.galaxy.service.usermanagement.Participant
 
getDependencies() - Method in class org.galaxy.model.EModelFragment
 
getDependencies() - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
getDescription() - Method in class org.galaxy.model.EModelFragment
 
getDescription() - Method in class org.galaxy.model.EProject
 
getDescription() - Method in class org.galaxy.model.ERole
 
getDescription() - Method in class org.galaxy.model.EWorkgroup
 
getDescription() - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
getDescription() - Method in class org.galaxy.service.projectmanagement.Project
 
getDescription() - Method in class org.galaxy.service.rolemanagement.Role
 
getDescription() - Method in class org.galaxy.service.workgroupmanagement.Workgroup
 
getEmail() - Method in class org.galaxy.model.EParticipant
 
getEmail() - Method in class org.galaxy.service.usermanagement.Participant
 
getEndDate() - Method in class org.galaxy.model.EProject
 
getEndDate() - Method in class org.galaxy.service.projectmanagement.Project
 
getFirstName() - Method in class org.galaxy.model.EParticipant
 
getFirstName() - Method in class org.galaxy.service.usermanagement.Participant
 
getFragments() - Method in class org.galaxy.model.EWorkgroup
 
getGalaxyId() - Method in class org.galaxy.model.EModelFragment
 
getGalaxyId() - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
getId() - Method in class org.galaxy.service.projectmanagement.Project
 
getId() - Method in class org.galaxy.service.rolemanagement.Role
 
getId() - Method in class org.galaxy.service.usermanagement.Participant
 
getId() - Method in class org.galaxy.service.workgroupmanagement.Workgroup
 
getImpactes() - Method in class org.galaxy.model.EModelFragment
 
getImpactes() - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
getLastName() - Method in class org.galaxy.model.EParticipant
 
getLastName() - Method in class org.galaxy.service.usermanagement.Participant
 
getLocalizedMessage() - Method in exception org.galaxy.service.modelfragment.InvalidPatternException
 
getLocalizedMessage() - Method in exception org.galaxy.utility.filerepository.IOFragmentException
 
getLocalizedMessage() - Method in exception org.galaxy.utility.fragmentanalyser.MalformedFragmentException
 
getMessage() - Method in exception org.galaxy.service.modelfragment.InvalidPatternException
 
getMessage() - Method in exception org.galaxy.utility.filerepository.IOFragmentException
 
getMessage() - Method in exception org.galaxy.utility.fragmentanalyser.MalformedFragmentException
 
getModelfragmentId() - Method in class org.galaxy.model.EModelFragment
 
getModelfragmentId() - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
getName() - Method in class org.galaxy.model.EModelFragment
 
getName() - Method in class org.galaxy.model.EProject
 
getName() - Method in class org.galaxy.model.ERole
 
getName() - Method in class org.galaxy.model.EWorkgroup
 
getName() - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
getName() - Method in class org.galaxy.service.projectmanagement.Project
 
getName() - Method in class org.galaxy.service.rolemanagement.Role
 
getName() - Method in class org.galaxy.service.workgroupmanagement.Workgroup
 
getOrganisation() - Method in class org.galaxy.model.EParticipant
 
getOrganisation() - Method in class org.galaxy.service.usermanagement.Participant
 
getParticipant() - Method in class org.galaxy.model.EProjectParticipant
 
getParticipantId() - Method in class org.galaxy.model.EParticipant
 
getParticipants() - Method in class org.galaxy.model.EProject
 
getParticipants() - Method in class org.galaxy.model.EWorkgroup
 
getParticipation() - Method in class org.galaxy.model.EParticipant
 
getParticipation() - Method in class org.galaxy.model.ERole
 
getPhone() - Method in class org.galaxy.model.EParticipant
 
getPhone() - Method in class org.galaxy.service.usermanagement.Participant
 
getProject() - Method in class org.galaxy.model.EProjectParticipant
 
getProjectId() - Method in class org.galaxy.model.EProject
 
getProjects() - Method in class org.galaxy.model.ERole
 
getRole() - Method in class org.galaxy.model.EProjectParticipant
 
getRoleId() - Method in class org.galaxy.model.ERole
 
getRoles() - Method in class org.galaxy.model.EProject
 
getStartDate() - Method in class org.galaxy.model.EProject
 
getStartDate() - Method in class org.galaxy.service.projectmanagement.Project
 
getString(String) - Static method in class org.galaxy.i18n.Messages
 
getString(String, String...) - Static method in class org.galaxy.i18n.Messages
 
getVersion() - Method in class org.galaxy.model.EModelFragment
 
getVersion() - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
getWorkgroupId() - Method in class org.galaxy.model.EWorkgroup
 
getWorkgroups() - Method in class org.galaxy.model.EModelFragment
 
getWorkgroups() - Method in class org.galaxy.model.EParticipant
 

I

id - Variable in class org.galaxy.service.projectmanagement.Project
 
id - Variable in class org.galaxy.service.rolemanagement.Role
 
id - Variable in class org.galaxy.service.usermanagement.Participant
 
id - Variable in class org.galaxy.service.workgroupmanagement.Workgroup
 
IFileRepository - Interface in org.galaxy.utility.filerepository
This interface contains services in order to manage physical ModelFragment repository into GalaxyServer.
IFragmentAnalyser - Interface in org.galaxy.utility.fragmentanalyser
This interface contains services in order to manipulate of ModelFragment archive such as extracting the metadata from the archive
IModelFragmentManagement - Interface in org.galaxy.service.modelfragment
This interface contains services in order to manage manage publication of Model Fragment on Galaxy server
impactes - Variable in class org.galaxy.model.EModelFragment
 
impactes - Variable in class org.galaxy.service.modelfragment.ModelFragmentData
 
InvalidPatternException - Exception in org.galaxy.service.modelfragment
Exception thrown when provided pattern does not comply with standard syntax.
InvalidPatternException(String) - Constructor for exception org.galaxy.service.modelfragment.InvalidPatternException
 
IOFragmentException - Exception in org.galaxy.utility.filerepository
Exception thrown when an error is triggered by manipulation of the file representing the model fragment
IOFragmentException(String) - Constructor for exception org.galaxy.utility.filerepository.IOFragmentException
 
IProjectManagement - Interface in org.galaxy.service.projectmanagement
This interface contains services in order to manage projects
IRoleManagement - Interface in org.galaxy.service.rolemanagement
This interface contains services in order to manage roles.
IUserManagement - Interface in org.galaxy.service.usermanagement
This interface contains services in order to manage users.
IWorkgroupManagement - Interface in org.galaxy.service.workgroupmanagement
This interface contains services in order to manage workgroup.

L

lastName - Variable in class org.galaxy.model.EParticipant
 
lastName - Variable in class org.galaxy.service.usermanagement.Participant
 

M

MalformedFragmentException - Exception in org.galaxy.utility.fragmentanalyser
 
MalformedFragmentException(String) - Constructor for exception org.galaxy.utility.fragmentanalyser.MalformedFragmentException
 
manager - Variable in class org.galaxy.service.modelfragment.ModelFragmentManagement
 
manager - Variable in class org.galaxy.service.projectmanagement.ProjectManagement
 
manager - Variable in class org.galaxy.service.rolemanagement.RoleManagement
 
manager - Variable in class org.galaxy.service.usermanagement.UserManagement
 
manager - Variable in class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
message - Variable in exception org.galaxy.service.modelfragment.InvalidPatternException
 
message - Variable in exception org.galaxy.utility.filerepository.IOFragmentException
 
message - Variable in exception org.galaxy.utility.fragmentanalyser.MalformedFragmentException
 
Messages - Class in org.galaxy.i18n
Service class dedicated to the management of internationalization
Messages() - Constructor for class org.galaxy.i18n.Messages
 
ModelFragmentData - Class in org.galaxy.service.modelfragment
Exchange data structure dedicated to ModelFraqment
ModelFragmentData() - Constructor for class org.galaxy.service.modelfragment.ModelFragmentData
 
modelfragmentId - Variable in class org.galaxy.model.EModelFragment
 
modelfragmentId - Variable in class org.galaxy.service.modelfragment.ModelFragmentData
 
ModelFragmentManagement - Class in org.galaxy.service.modelfragment
Implementation of IModelFragmentManagement services dedicated to ModelFragment management
ModelFragmentManagement() - Constructor for class org.galaxy.service.modelfragment.ModelFragmentManagement
 

N

name - Variable in class org.galaxy.model.EModelFragment
 
name - Variable in class org.galaxy.model.EProject
 
name - Variable in class org.galaxy.model.ERole
 
name - Variable in class org.galaxy.model.EWorkgroup
 
name - Variable in class org.galaxy.service.modelfragment.ModelFragmentData
 
name - Variable in class org.galaxy.service.projectmanagement.Project
 
name - Variable in class org.galaxy.service.rolemanagement.Role
 
name - Variable in class org.galaxy.service.workgroupmanagement.Workgroup
 

O

org - package org
 
org.galaxy - package org.galaxy
 
org.galaxy.i18n - package org.galaxy.i18n
 
org.galaxy.model - package org.galaxy.model
 
org.galaxy.service - package org.galaxy.service
 
org.galaxy.service.modelfragment - package org.galaxy.service.modelfragment
 
org.galaxy.service.projectmanagement - package org.galaxy.service.projectmanagement
 
org.galaxy.service.rolemanagement - package org.galaxy.service.rolemanagement
 
org.galaxy.service.usermanagement - package org.galaxy.service.usermanagement
 
org.galaxy.service.workgroupmanagement - package org.galaxy.service.workgroupmanagement
 
org.galaxy.utility - package org.galaxy.utility
 
org.galaxy.utility.filerepository - package org.galaxy.utility.filerepository
 
org.galaxy.utility.fragmentanalyser - package org.galaxy.utility.fragmentanalyser
 
organisation - Variable in class org.galaxy.model.EParticipant
 
organisation - Variable in class org.galaxy.service.usermanagement.Participant
 

P

participant - Variable in class org.galaxy.model.EProjectParticipant
 
Participant - Class in org.galaxy.service.usermanagement
Exchange data structure dedicated to Participant
Participant() - Constructor for class org.galaxy.service.usermanagement.Participant
 
participantId - Variable in class org.galaxy.model.EParticipant
 
participants - Variable in class org.galaxy.model.EProject
 
participants - Variable in class org.galaxy.model.EWorkgroup
 
participation - Variable in class org.galaxy.model.EParticipant
 
participation - Variable in class org.galaxy.model.ERole
 
phone - Variable in class org.galaxy.model.EParticipant
 
phone - Variable in class org.galaxy.service.usermanagement.Participant
 
project - Variable in class org.galaxy.model.EProjectParticipant
 
Project - Class in org.galaxy.service.projectmanagement
Exchange data structure dedicated to Project
Project() - Constructor for class org.galaxy.service.projectmanagement.Project
 
projectId - Variable in class org.galaxy.model.EProject
 
ProjectManagement - Class in org.galaxy.service.projectmanagement
Implementation of IProjectManagement services dedicated to projects management
ProjectManagement() - Constructor for class org.galaxy.service.projectmanagement.ProjectManagement
 
projects - Variable in class org.galaxy.model.ERole
 
publish(DataHandler) - Method in interface org.galaxy.service.modelfragment.IModelFragmentManagement
Takes a Model Fragment object and publishes it in the Galaxy repository, as a single archive file
publish(DataHandler) - Method in class org.galaxy.service.modelfragment.ModelFragmentManagement
 

R

removeParticipant(Integer, Integer, List<Integer>) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Remove specified Participant from Project with specified role Roles must be roles of project
removeParticipant(Integer, Integer, List<Integer>) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
removeParticipant(Integer, Integer) - Method in interface org.galaxy.service.workgroupmanagement.IWorkgroupManagement
Remove specified Participant of specified Workgroup
removeParticipant(Integer, Integer) - Method in class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
removeParticipants(Integer, List<Integer>, List<Integer>) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Remove specified participant from Project
removeParticipants(Integer, List<Integer>, List<Integer>) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
removeParticipants(Integer, List<Integer>) - Method in interface org.galaxy.service.workgroupmanagement.IWorkgroupManagement
Remove specified Participants of specified Workgroup
removeParticipants(Integer, List<Integer>) - Method in class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
removeRole(Integer, Integer) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Add specified Role of specified Project
removeRole(Integer, Integer) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
removeRoles(Integer, List<Integer>) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Remove List of roles to Project
removeRoles(Integer, List<Integer>) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
repository - Variable in class org.galaxy.service.modelfragment.ModelFragmentManagement
 
RESOURCE_BUNDLE - Static variable in class org.galaxy.i18n.Messages
 
retiveFile(String, String) - Method in class org.galaxy.utility.filerepository.FileRepository
 
retiveFile(String, String) - Method in interface org.galaxy.utility.filerepository.IFileRepository
Retrieving a Model Fragment from the repository
retrieve(String, String) - Method in interface org.galaxy.service.modelfragment.IModelFragmentManagement
Retrieves a Model Fragment from the Galaxy repository, based on its id.
retrieve(String, String) - Method in class org.galaxy.service.modelfragment.ModelFragmentManagement
 
role - Variable in class org.galaxy.model.EProjectParticipant
 
Role - Class in org.galaxy.service.rolemanagement
Exchange data structure dedicated to Roles
Role() - Constructor for class org.galaxy.service.rolemanagement.Role
 
roleId - Variable in class org.galaxy.model.ERole
 
RoleManagement - Class in org.galaxy.service.rolemanagement
Implementation of IUserManagement services dedicated to role management
RoleManagement() - Constructor for class org.galaxy.service.rolemanagement.RoleManagement
 
roles - Variable in class org.galaxy.model.EProject
 

S

setAddress(String) - Method in class org.galaxy.model.EParticipant
 
setAddress(String) - Method in class org.galaxy.service.usermanagement.Participant
 
setCategory(String) - Method in class org.galaxy.model.ERole
 
setCategory(String) - Method in class org.galaxy.service.rolemanagement.Role
 
setCountry(String) - Method in class org.galaxy.model.EParticipant
 
setCountry(String) - Method in class org.galaxy.service.usermanagement.Participant
 
setDependencies(List<EModelFragment>) - Method in class org.galaxy.model.EModelFragment
 
setDependencies(List<ModelFragmentData>) - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
setDescription(String) - Method in class org.galaxy.model.EModelFragment
 
setDescription(String) - Method in class org.galaxy.model.EProject
 
setDescription(String) - Method in class org.galaxy.model.ERole
 
setDescription(String) - Method in class org.galaxy.model.EWorkgroup
 
setDescription(String) - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
setDescription(String) - Method in class org.galaxy.service.projectmanagement.Project
 
setDescription(String) - Method in class org.galaxy.service.rolemanagement.Role
 
setDescription(String) - Method in class org.galaxy.service.workgroupmanagement.Workgroup
 
setEmail(String) - Method in class org.galaxy.model.EParticipant
 
setEmail(String) - Method in class org.galaxy.service.usermanagement.Participant
 
setEndDate(String) - Method in class org.galaxy.model.EProject
 
setEndDate(String) - Method in class org.galaxy.service.projectmanagement.Project
 
setFirstName(String) - Method in class org.galaxy.model.EParticipant
 
setFirstName(String) - Method in class org.galaxy.service.usermanagement.Participant
 
setFragments(List<EModelFragment>) - Method in class org.galaxy.model.EWorkgroup
 
setGalaxyId(String) - Method in class org.galaxy.model.EModelFragment
 
setGalaxyId(String) - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
setId(Integer) - Method in class org.galaxy.service.projectmanagement.Project
 
setId(Integer) - Method in class org.galaxy.service.rolemanagement.Role
 
setId(Integer) - Method in class org.galaxy.service.usermanagement.Participant
 
setId(Integer) - Method in class org.galaxy.service.workgroupmanagement.Workgroup
 
setImpactes(List<EModelFragment>) - Method in class org.galaxy.model.EModelFragment
 
setImpactes(List<ModelFragmentData>) - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
setLastName(String) - Method in class org.galaxy.model.EParticipant
 
setLastName(String) - Method in class org.galaxy.service.usermanagement.Participant
 
setModelfragmentId(Integer) - Method in class org.galaxy.model.EModelFragment
 
setModelfragmentId(Integer) - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
setName(String) - Method in class org.galaxy.model.EModelFragment
 
setName(String) - Method in class org.galaxy.model.EProject
 
setName(String) - Method in class org.galaxy.model.ERole
 
setName(String) - Method in class org.galaxy.model.EWorkgroup
 
setName(String) - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
setName(String) - Method in class org.galaxy.service.projectmanagement.Project
 
setName(String) - Method in class org.galaxy.service.rolemanagement.Role
 
setName(String) - Method in class org.galaxy.service.workgroupmanagement.Workgroup
 
setOrganisation(String) - Method in class org.galaxy.model.EParticipant
 
setOrganisation(String) - Method in class org.galaxy.service.usermanagement.Participant
 
setParticipant(EParticipant) - Method in class org.galaxy.model.EProjectParticipant
 
setParticipantId(Integer) - Method in class org.galaxy.model.EParticipant
 
setParticipants(List<EProjectParticipant>) - Method in class org.galaxy.model.EProject
 
setParticipants(List<EParticipant>) - Method in class org.galaxy.model.EWorkgroup
 
setParticipation(List<EProjectParticipant>) - Method in class org.galaxy.model.EParticipant
 
setParticipation(List<EProjectParticipant>) - Method in class org.galaxy.model.ERole
 
setPhone(String) - Method in class org.galaxy.model.EParticipant
 
setPhone(String) - Method in class org.galaxy.service.usermanagement.Participant
 
setProject(EProject) - Method in class org.galaxy.model.EProjectParticipant
 
setProjectId(Integer) - Method in class org.galaxy.model.EProject
 
setProjects(List<EProject>) - Method in class org.galaxy.model.ERole
 
setRole(ERole) - Method in class org.galaxy.model.EProjectParticipant
 
setRoleId(Integer) - Method in class org.galaxy.model.ERole
 
setRoles(List<ERole>) - Method in class org.galaxy.model.EProject
 
setStartDate(String) - Method in class org.galaxy.model.EProject
 
setStartDate(String) - Method in class org.galaxy.service.projectmanagement.Project
 
setVersion(String) - Method in class org.galaxy.model.EModelFragment
 
setVersion(String) - Method in class org.galaxy.service.modelfragment.ModelFragmentData
 
setWorkgroupId(Integer) - Method in class org.galaxy.model.EWorkgroup
 
setWorkgroups(List<EWorkgroup>) - Method in class org.galaxy.model.EModelFragment
 
setWorkgroups(List<EWorkgroup>) - Method in class org.galaxy.model.EParticipant
 
startDate - Variable in class org.galaxy.model.EProject
 
startDate - Variable in class org.galaxy.service.projectmanagement.Project
 
storeFile(File, String, String) - Method in class org.galaxy.utility.filerepository.FileRepository
 
storeFile(File, String, String) - Method in interface org.galaxy.utility.filerepository.IFileRepository
Storing a ModelFragment in the repository

U

updateParticipant(Participant) - Method in interface org.galaxy.service.usermanagement.IUserManagement
Update the given participant from the system
updateParticipant(Participant) - Method in class org.galaxy.service.usermanagement.UserManagement
 
updateProject(Project) - Method in interface org.galaxy.service.projectmanagement.IProjectManagement
Update the given project from the system
updateProject(Project) - Method in class org.galaxy.service.projectmanagement.ProjectManagement
 
updateRole(Role) - Method in interface org.galaxy.service.rolemanagement.IRoleManagement
Update the given role from the system
updateRole(Role) - Method in class org.galaxy.service.rolemanagement.RoleManagement
 
updateWorkgroup(Workgroup) - Method in interface org.galaxy.service.workgroupmanagement.IWorkgroupManagement
Update the given workgroup from the system
updateWorkgroup(Workgroup) - Method in class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
UserManagement - Class in org.galaxy.service.usermanagement
Implementation of IUserManagement services dedicated to user management
UserManagement() - Constructor for class org.galaxy.service.usermanagement.UserManagement
 

V

validate(File) - Method in class org.galaxy.utility.fragmentanalyser.FragmentAnalyser
 
validate(File) - Method in interface org.galaxy.utility.fragmentanalyser.IFragmentAnalyser
Validation of ModelFragment
validateMetadata(ModelFragment) - Method in class org.galaxy.utility.fragmentanalyser.FragmentAnalyser
 
validateMetadata(ModelFragment) - Method in interface org.galaxy.utility.fragmentanalyser.IFragmentAnalyser
Validation of metadata associated with ModelFragment
version - Variable in class org.galaxy.model.EModelFragment
 
version - Variable in class org.galaxy.service.modelfragment.ModelFragmentData
 

W

Workgroup - Class in org.galaxy.service.workgroupmanagement
Exchange data structure dedicated to Workgroup
Workgroup() - Constructor for class org.galaxy.service.workgroupmanagement.Workgroup
 
workgroupId - Variable in class org.galaxy.model.EWorkgroup
 
WorkgroupManagement - Class in org.galaxy.service.workgroupmanagement
Implementation of IWorkgroupManagement services dedicated to workgroup management
WorkgroupManagement() - Constructor for class org.galaxy.service.workgroupmanagement.WorkgroupManagement
 
workgroups - Variable in class org.galaxy.model.EModelFragment
 
workgroups - Variable in class org.galaxy.model.EParticipant
 
A C D E F G I L M N O P R S U V W