Package | Description |
---|---|
net.sourceforge.seqware.common.business |
Looks like auto-generated classes for Hibernate.
|
net.sourceforge.seqware.common.business.impl |
Looks like auto-generated implementation for Hibernate classes.
|
net.sourceforge.seqware.common.dao |
More hibernate auto-generated.
|
net.sourceforge.seqware.common.dao.hibernate |
More hibernate auto-generated.
|
net.sourceforge.seqware.common.model |
Hibernate model classes for the metadb.
|
net.sourceforge.seqware.common.security |
Interface that unifies model objects that have the concept of permissions.
|
net.sourceforge.seqware.webservice.resources |
Base classes for web resources.
|
net.sourceforge.solexatools |
Portal stuff, to be assessed.
|
net.sourceforge.solexatools.util |
Portal stuff, to be assessed.
|
net.sourceforge.solexatools.webapp.controller |
Portal stuff, to be assessed.
|
Modifier and Type | Method and Description |
---|---|
Registration |
RegistrationService.updateDetached(Registration registration)
updateDetached.
|
Modifier and Type | Method and Description |
---|---|
Integer |
ExperimentService.insert(Registration registration,
Experiment experiment)
insert.
|
Integer |
FileService.insert(Registration registration,
File file)
insert.
|
Integer |
InvoiceService.insert(Registration registration,
Invoice invoice)
insert.
|
Integer |
IUSService.insert(Registration registration,
IUS ius)
insert.
|
Integer |
LaneService.insert(Registration registration,
Lane lane)
insert.
|
Integer |
ProcessingService.insert(Registration registration,
Processing processing)
insert.
|
Integer |
SampleService.insert(Registration registration,
Sample sample)
insert.
|
Integer |
SequencerRunService.insert(Registration registration,
SequencerRun sequencerRun)
insert.
|
void |
ProcessingService.insert(Registration registration,
SequencerRun sequencerRun,
Processing processing)
insert.
|
Integer |
SequencerRunService.insert(Registration registration,
SequencerRunWizardDTO sequencerRun)
insert.
|
Integer |
StudyService.insert(Registration registration,
Study study)
insert.
|
Integer |
WorkflowService.insert(Registration registration,
Workflow workflow)
insert.
|
Integer |
WorkflowParamService.insert(Registration registration,
WorkflowParam workflowParam)
insert.
|
Integer |
WorkflowParamValueService.insert(Registration registration,
WorkflowParamValue workflowParamValue)
insert.
|
Integer |
WorkflowRunService.insert(Registration registration,
WorkflowRun workflowRun)
insert.
|
void |
WorkflowRunParamService.insert(Registration registration,
WorkflowRunParam workflowRunParam)
insert.
|
Integer |
WorkflowRunService.insert(Registration registration,
WorkflowRun workflowRun,
SortedSet<WorkflowRunParam> workflowRunParams,
Map<String,List<File>> allSelectedFiles)
insert.
|
Integer |
LaneService.insertLane(Registration registration,
Sample sample,
UploadSequence uploadSequence,
FileType fileType)
insertLane.
|
List<Experiment> |
ExperimentService.list(Registration registration)
list.
|
List<ExperimentLibraryDesign> |
ExperimentLibraryDesignService.list(Registration registration)
list.
|
List<Workflow> |
WorkflowService.list(Registration registration)
list.
|
List<Platform> |
PlatformService.list(Registration registration)
list.
|
List<LibrarySelection> |
LibrarySelectionService.list(Registration registration)
list.
|
List<Organism> |
OrganismService.list(Registration registration)
list.
|
List<Invoice> |
InvoiceService.list(Registration registration)
list.
|
List<Study> |
StudyService.list(Registration registration)
list.
|
List<SequencerRun> |
SequencerRunService.list(Registration registration)
list.
|
List<WorkflowRun> |
WorkflowRunService.list(Registration registration)
list.
|
List<LibraryStrategy> |
LibraryStrategyService.list(Registration registration)
list.
|
List<LibrarySource> |
LibrarySourceService.list(Registration registration)
list.
|
List<StudyType> |
StudyTypeService.list(Registration registration)
list.
|
List<Study> |
StudyService.list(Registration registration,
Boolean isAcs)
list.
|
List<SequencerRun> |
SequencerRunService.list(Registration registration,
Boolean isAsc)
list.
|
List<WorkflowRun> |
WorkflowRunService.list(Registration registration,
Boolean isAsc)
list.
|
List<Invoice> |
InvoiceService.list(Registration registration,
InvoiceState state)
list.
|
List<File> |
LaneService.listFile(Registration reqistration,
String typeNode,
List<File> list,
String[] ids,
String[] statuses)
listFile.
|
List<Workflow> |
WorkflowService.listMyShared(Registration registration)
listMyShared.
|
List<WorkflowRun> |
WorkflowRunService.listMyShared(Registration registration)
listMyShared.
|
List<Study> |
StudyService.listMyShared(Registration registration,
Boolean isAcs)
listMyShared.
|
List<WorkflowRun> |
WorkflowRunService.listMyShared(Registration registration,
Boolean isAsc)
listMyShared.
|
List<Workflow> |
WorkflowRunService.listRelatedWorkflows(Registration registration)
listRelatedWorkflows.
|
List<WorkflowRun> |
WorkflowRunService.listRunning(Registration registration)
listRunning.
|
List<WorkflowRun> |
WorkflowRunService.listRunning(Registration registration,
Boolean isAsc)
listRunning.
|
List<Sample> |
SampleService.listSample(Registration registration)
listSample.
|
List<Workflow> |
WorkflowService.listSharedWithMe(Registration registration)
listSharedWithMe.
|
List<Study> |
StudyService.listSharedWithMe(Registration registration)
listSharedWithMe.
|
List<WorkflowRun> |
WorkflowRunService.listSharedWithMe(Registration registration)
listSharedWithMe.
|
List<Study> |
StudyService.listSharedWithMe(Registration registration,
Boolean isAcs)
listSharedWithMe.
|
List<WorkflowRun> |
WorkflowRunService.listSharedWithMe(Registration registration,
Boolean isAsc)
listSharedWithMe.
|
List<WorkflowRun> |
WorkflowRunService.listSharedWithMeWithSample(Registration registration)
listSharedWithMeWithSample.
|
List<Study> |
StudyService.listStudyHasFile(Registration registration,
String metaType,
Boolean isAcs)
listStudyHasFile.
|
void |
ExperimentService.update(Registration registration,
Experiment experiment)
update.
|
void |
FileService.update(Registration registration,
File file)
update.
|
void |
InvoiceService.update(Registration registration,
Invoice invoice)
update.
|
void |
IUSService.update(Registration registration,
IUS ius)
update.
|
void |
LaneService.update(Registration registration,
Lane lane)
update.
|
void |
ProcessingService.update(Registration registration,
Processing processing)
update.
|
void |
SampleService.update(Registration registration,
Sample sample)
update.
|
void |
SequencerRunService.update(Registration registration,
SequencerRun sequencerRun)
update.
|
void |
StudyService.update(Registration registration,
Study study)
update.
|
void |
WorkflowService.update(Registration registration,
Workflow workflow)
update.
|
void |
WorkflowParamService.update(Registration registration,
WorkflowParam workflowParam)
update.
|
void |
WorkflowParamValueService.update(Registration registration,
WorkflowParamValue workflowParamValue)
update.
|
void |
WorkflowRunService.update(Registration registration,
WorkflowRun workflowRun)
update.
|
void |
WorkflowRunService.update(Registration registration,
WorkflowRun workflowRun,
List<Integer> laneIds)
update.
|
void |
WorkflowRunParamService.update(Registration registration,
WorkflowRunParam workflowRunParam)
update.
|
Registration |
RegistrationService.updateDetached(Registration registration)
updateDetached.
|
Experiment |
ExperimentService.updateDetached(Registration registration,
Experiment experiment)
updateDetached.
|
File |
FileService.updateDetached(Registration registration,
File file)
updateDetached.
|
Invoice |
InvoiceService.updateDetached(Registration registration,
Invoice invoice)
updateDetached.
|
IUS |
IUSService.updateDetached(Registration registration,
IUS ius)
updateDetached.
|
Lane |
LaneService.updateDetached(Registration registration,
Lane lane)
updateDetached.
|
Processing |
ProcessingService.updateDetached(Registration registration,
Processing processing)
updateDetached.
|
Sample |
SampleService.updateDetached(Registration registration,
Sample sample)
updateDetached.
|
SequencerRun |
SequencerRunService.updateDetached(Registration registration,
SequencerRun sequencerRun)
updateDetached.
|
Study |
StudyService.updateDetached(Registration registration,
Study study)
updateDetached.
|
Workflow |
WorkflowService.updateDetached(Registration registration,
Workflow workflow)
updateDetached.
|
WorkflowParam |
WorkflowParamService.updateDetached(Registration registration,
WorkflowParam workflowParam)
updateDetached.
|
WorkflowParamValue |
WorkflowParamValueService.updateDetached(Registration registration,
WorkflowParamValue workflowParamValue)
updateDetached.
|
WorkflowRunParam |
WorkflowRunParamService.updateDetached(Registration registration,
WorkflowRunParam workflowRunParam)
updateDetached.
|
void |
FileUploadService.uploadFile(Experiment experiment,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
void |
FileUploadService.uploadFile(IUS ius,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
void |
FileUploadService.uploadFile(Lane lane,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
void |
FileUploadService.uploadFile(Processing processing,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
void |
FileUploadService.uploadFile(Sample sample,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
void |
FileUploadService.uploadFile(SequencerRun sequencerRun,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
void |
FileUploadService.uploadFile(Study study,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
Modifier and Type | Method and Description |
---|---|
Registration |
RegistrationServiceImpl.updateDetached(Registration registration)
updateDetached.
|
Modifier and Type | Method and Description |
---|---|
Integer |
ExperimentServiceImpl.insert(Registration registration,
Experiment experiment)
insert.
|
Integer |
FileServiceImpl.insert(Registration registration,
File file)
insert.
|
Integer |
InvoiceServiceImpl.insert(Registration registration,
Invoice invoice)
insert.
|
Integer |
IUSServiceImpl.insert(Registration registration,
IUS ius)
insert.
|
Integer |
LaneServiceImpl.insert(Registration registration,
Lane lane)
insert.
|
Integer |
ProcessingServiceImpl.insert(Registration registration,
Processing processing)
insert.
|
Integer |
SampleServiceImpl.insert(Registration registration,
Sample sample)
insert.
|
Integer |
SequencerRunServiceImpl.insert(Registration registration,
SequencerRun sequencerRun)
insert.
|
void |
ProcessingServiceImpl.insert(Registration registration,
SequencerRun sequencerRun,
Processing processing)
insert.
|
Integer |
SequencerRunServiceImpl.insert(Registration registration,
SequencerRunWizardDTO sequencerRun)
insert.
|
Integer |
StudyServiceImpl.insert(Registration registration,
Study study)
insert.
|
Integer |
WorkflowServiceImpl.insert(Registration registration,
Workflow workflow)
insert.
|
Integer |
WorkflowParamServiceImpl.insert(Registration registration,
WorkflowParam workflowParam)
insert.
|
Integer |
WorkflowParamValueServiceImpl.insert(Registration registration,
WorkflowParamValue workflowParamValue)
insert.
|
Integer |
WorkflowRunServiceImpl.insert(Registration registration,
WorkflowRun workflowRun)
insert.
|
void |
WorkflowRunParamServiceImpl.insert(Registration registration,
WorkflowRunParam workflowRunParam)
insert.
|
Integer |
WorkflowRunServiceImpl.insert(Registration registration,
WorkflowRun workflowRun,
SortedSet<WorkflowRunParam> workflowRunParams,
Map<String,List<File>> allSelectedFiles)
insert.
|
Integer |
LaneServiceImpl.insertLane(Registration registration,
Sample sample,
UploadSequence uploadSeqence,
FileType fileType)
insertLane.
|
List<Study> |
StudyServiceImpl.list(Registration registration)
list.
|
List<Invoice> |
InvoiceServiceImpl.list(Registration registration)
list.
|
List<WorkflowRun> |
WorkflowRunServiceImpl.list(Registration registration)
list.
|
List<LibrarySource> |
LibrarySourceServiceImpl.list(Registration registration)
list.
|
List<Workflow> |
WorkflowServiceImpl.list(Registration registration)
list.
|
List<LibrarySelection> |
LibrarySelectionServiceImpl.list(Registration registration)
list.
|
List<Experiment> |
ExperimentServiceImpl.list(Registration registration)
list.
|
List<Organism> |
OrganismServiceImpl.list(Registration registration)
list.
|
List<StudyType> |
StudyTypeServiceImpl.list(Registration registration)
list.
|
List<LibraryStrategy> |
LibraryStrategyServiceImpl.list(Registration registration)
list.
|
List<SequencerRun> |
SequencerRunServiceImpl.list(Registration registration)
list.
|
List<ExperimentLibraryDesign> |
ExperimentLibraryDesignServiceImpl.list(Registration registration)
list.
|
List<Platform> |
PlatformServiceImpl.list(Registration registration)
list.
|
List<Study> |
StudyServiceImpl.list(Registration registration,
Boolean isAcs)
list.
|
List<WorkflowRun> |
WorkflowRunServiceImpl.list(Registration registration,
Boolean isAsc)
list.
|
List<SequencerRun> |
SequencerRunServiceImpl.list(Registration registration,
Boolean isAsc)
list.
|
List<Invoice> |
InvoiceServiceImpl.list(Registration registration,
InvoiceState state)
list.
|
List<File> |
LaneServiceImpl.listFile(Registration reqistration,
String typeNode,
List<File> list,
String[] ids,
String[] statuses)
listFile.
|
List<WorkflowRun> |
WorkflowRunServiceImpl.listMyShared(Registration registration)
listMyShared.
|
List<Workflow> |
WorkflowServiceImpl.listMyShared(Registration registration)
listMyShared.
|
List<Study> |
StudyServiceImpl.listMyShared(Registration registration,
Boolean isAcs)
listMyShared.
|
List<WorkflowRun> |
WorkflowRunServiceImpl.listMyShared(Registration registration,
Boolean isAsc)
listMyShared.
|
List<Workflow> |
WorkflowRunServiceImpl.listRelatedWorkflows(Registration registration)
listRelatedWorkflows.
|
List<WorkflowRun> |
WorkflowRunServiceImpl.listRunning(Registration registration)
listRunning.
|
List<WorkflowRun> |
WorkflowRunServiceImpl.listRunning(Registration registration,
Boolean isAsc)
listRunning.
|
List<Sample> |
SampleServiceImpl.listSample(Registration registration)
listSample.
|
List<Study> |
StudyServiceImpl.listSharedWithMe(Registration registration)
listSharedWithMe.
|
List<WorkflowRun> |
WorkflowRunServiceImpl.listSharedWithMe(Registration registration)
listSharedWithMe.
|
List<Workflow> |
WorkflowServiceImpl.listSharedWithMe(Registration registration)
listSharedWithMe.
|
List<Study> |
StudyServiceImpl.listSharedWithMe(Registration registration,
Boolean isAcs)
listSharedWithMe.
|
List<WorkflowRun> |
WorkflowRunServiceImpl.listSharedWithMe(Registration registration,
Boolean isAsc)
listSharedWithMe.
|
List<WorkflowRun> |
WorkflowRunServiceImpl.listSharedWithMeWithSample(Registration registration)
listSharedWithMeWithSample.
|
List<Study> |
StudyServiceImpl.listStudyHasFile(Registration registration,
String metaType,
Boolean isAsc)
listStudyHasFile.
|
void |
ExperimentServiceImpl.update(Registration registration,
Experiment experiment)
update.
|
void |
FileServiceImpl.update(Registration registration,
File file)
update.
|
void |
InvoiceServiceImpl.update(Registration registration,
Invoice invoice)
update.
|
void |
IUSServiceImpl.update(Registration registration,
IUS ius)
update.
|
void |
LaneServiceImpl.update(Registration registration,
Lane lane)
update.
|
void |
ProcessingServiceImpl.update(Registration registration,
Processing processing)
update.
|
void |
SampleServiceImpl.update(Registration registration,
Sample sample)
update.
|
void |
SequencerRunServiceImpl.update(Registration registration,
SequencerRun sequencerRun)
update.
|
void |
StudyServiceImpl.update(Registration registration,
Study study)
update.
|
void |
WorkflowServiceImpl.update(Registration registration,
Workflow workflow)
update.
|
void |
WorkflowParamServiceImpl.update(Registration registration,
WorkflowParam workflowParam)
update.
|
void |
WorkflowParamValueServiceImpl.update(Registration registration,
WorkflowParamValue workflowParamValue)
update.
|
void |
WorkflowRunServiceImpl.update(Registration registration,
WorkflowRun workflowRun)
update.
|
void |
WorkflowRunServiceImpl.update(Registration registration,
WorkflowRun workflowRun,
List<Integer> laneIds)
update.
|
void |
WorkflowRunParamServiceImpl.update(Registration registration,
WorkflowRunParam workflowRunParam)
update.
|
Registration |
RegistrationServiceImpl.updateDetached(Registration registration)
updateDetached.
|
Experiment |
ExperimentServiceImpl.updateDetached(Registration registration,
Experiment experiment)
updateDetached.
|
File |
FileServiceImpl.updateDetached(Registration registration,
File file)
updateDetached.
|
Invoice |
InvoiceServiceImpl.updateDetached(Registration registration,
Invoice invoice)
updateDetached.
|
IUS |
IUSServiceImpl.updateDetached(Registration registration,
IUS ius)
updateDetached.
|
Lane |
LaneServiceImpl.updateDetached(Registration registration,
Lane lane)
updateDetached.
|
Processing |
ProcessingServiceImpl.updateDetached(Registration registration,
Processing processing)
updateDetached.
|
Sample |
SampleServiceImpl.updateDetached(Registration registration,
Sample sample)
updateDetached.
|
SequencerRun |
SequencerRunServiceImpl.updateDetached(Registration registration,
SequencerRun sequencerRun)
updateDetached.
|
Study |
StudyServiceImpl.updateDetached(Registration registration,
Study study)
updateDetached.
|
Workflow |
WorkflowServiceImpl.updateDetached(Registration registration,
Workflow workflow)
updateDetached.
|
WorkflowParam |
WorkflowParamServiceImpl.updateDetached(Registration registration,
WorkflowParam workflowParam)
updateDetached.
|
WorkflowParamValue |
WorkflowParamValueServiceImpl.updateDetached(Registration registration,
WorkflowParamValue workflowParamValue)
updateDetached.
|
WorkflowRunParam |
WorkflowRunParamServiceImpl.updateDetached(Registration registration,
WorkflowRunParam workflowRunParam)
updateDetached.
|
Integer |
LaneServiceImpl.updateLane(Sample sample,
org.springframework.web.multipart.MultipartFile fileOne,
org.springframework.web.multipart.MultipartFile fileTwo,
String typeFile,
String folderStore,
Registration registration)
updateLane.
|
void |
FileUploadServiceImpl.uploadFile(Experiment experiment,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
void |
FileUploadServiceImpl.uploadFile(IUS ius,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
void |
FileUploadServiceImpl.uploadFile(Lane lane,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
void |
FileUploadServiceImpl.uploadFile(Processing processing,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
void |
FileUploadServiceImpl.uploadFile(Sample sample,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
void |
FileUploadServiceImpl.uploadFile(SequencerRun sequencerRun,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
void |
FileUploadServiceImpl.uploadFile(Study study,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
Modifier and Type | Method and Description |
---|---|
Registration |
RegistrationDAO.findByEmailAddress(String emailAddress)
findByEmailAddress.
|
Registration |
RegistrationDAO.findByEmailAddressAndPassword(String emailAddress,
String password)
findByEmailAddressAndPassword.
|
Registration |
RegistrationDAO.updateDetached(Registration registration)
updateDetached.
|
Modifier and Type | Method and Description |
---|---|
void |
RegistrationDAO.insert(Registration registration)
insert.
|
Integer |
ExperimentDAO.insert(Registration registration,
Experiment sequencerRun)
insert.
|
Integer |
FileDAO.insert(Registration registration,
File file)
insert.
|
Integer |
InvoiceDAO.insert(Registration registration,
Invoice invoice)
insert.
|
Integer |
IUSDAO.insert(Registration registration,
IUS obj)
insert.
|
Integer |
LaneDAO.insert(Registration registration,
Lane lane)
insert.
|
Integer |
ProcessingDAO.insert(Registration registration,
Processing processing)
insert.
|
Integer |
SampleDAO.insert(Registration registration,
Sample sample)
insert.
|
Integer |
SequencerRunDAO.insert(Registration registration,
SequencerRun sequencerRun)
insert.
|
Integer |
SequencerRunDAO.insert(Registration registration,
SequencerRunWizardDTO sequencerRun)
insert.
|
Integer |
StudyDAO.insert(Registration registration,
Study sequencerRun)
insert.
|
Integer |
WorkflowDAO.insert(Registration registration,
Workflow workflow)
insert.
|
Integer |
WorkflowParamDAO.insert(Registration registration,
WorkflowParam workflowParam)
insert.
|
Integer |
WorkflowParamValueDAO.insert(Registration registration,
WorkflowParamValue workflowParamValue)
insert.
|
Integer |
WorkflowRunDAO.insert(Registration registration,
WorkflowRun workflowRun)
insert.
|
void |
WorkflowRunParamDAO.insert(Registration registration,
WorkflowRunParam workflowRunParam)
insert.
|
void |
WorkflowRunParamDAO.insertFilesAsWorkflowRunParam(Registration registration,
WorkflowRun workflowRun,
Map<String,List<File>> files)
insertFilesAsWorkflowRunParam.
|
List<Invoice> |
InvoiceDAO.list(Registration registration)
list.
|
List<LibrarySelection> |
LibrarySelectionDAO.list(Registration registration)
list.
|
List<LibraryStrategy> |
LibraryStrategyDAO.list(Registration registration)
list.
|
List<Organism> |
OrganismDAO.list(Registration registration)
list.
|
List<Platform> |
PlatformDAO.list(Registration registration)
list.
|
List<Experiment> |
ExperimentDAO.list(Registration registration)
list.
|
List<ExperimentLibraryDesign> |
ExperimentLibraryDesignDAO.list(Registration registration)
list.
|
List<Workflow> |
WorkflowDAO.list(Registration registration)
list.
|
List<LibrarySource> |
LibrarySourceDAO.list(Registration registration)
list.
|
List<StudyType> |
StudyTypeDAO.list(Registration registration)
list.
|
List<Study> |
StudyDAO.list(Registration registration,
Boolean isAcs)
list.
|
List<WorkflowRun> |
WorkflowRunDAO.list(Registration registration,
Boolean isAsc)
list.
|
List<SequencerRun> |
SequencerRunDAO.list(Registration registration,
Boolean isAsc)
list.
|
List<Invoice> |
InvoiceDAO.list(Registration registration,
InvoiceState state)
list.
|
List<Workflow> |
WorkflowDAO.listMyShared(Registration registration)
listMyShared.
|
List<Study> |
StudyDAO.listMyShared(Registration registration,
Boolean isAcs)
listMyShared.
|
List<WorkflowRun> |
WorkflowRunDAO.listMyShared(Registration registration,
Boolean isAsc)
listMyShared.
|
List<Workflow> |
WorkflowRunDAO.listRelatedWorkflows(Registration registration)
listRelatedWorkflows.
|
List<WorkflowRun> |
WorkflowRunDAO.listRunning(Registration registration,
Boolean isAsc)
listRunning.
|
List<Sample> |
SampleDAO.listSample(Registration registration)
listSample.
|
List<Workflow> |
WorkflowDAO.listSharedWithMe(Registration registration)
listSharedWithMe.
|
List<Study> |
StudyDAO.listSharedWithMe(Registration registration,
Boolean isAcs)
listSharedWithMe.
|
List<WorkflowRun> |
WorkflowRunDAO.listSharedWithMe(Registration registration,
Boolean isAsc)
listSharedWithMe.
|
List<Study> |
StudyDAO.listStudyHasFile(Registration registration,
String metaType,
Boolean iaAsc)
listStudyHasFile.
|
File |
FileDAO.saveFile(org.springframework.web.multipart.MultipartFile uploadFile,
String folderStore,
Registration owner)
saveFile.
|
void |
RegistrationDAO.update(Registration registration)
update.
|
void |
ExperimentDAO.update(Registration registration,
Experiment experiment)
update.
|
void |
FileDAO.update(Registration registration,
File file)
update.
|
void |
InvoiceDAO.update(Registration registration,
Invoice invoice)
update.
|
void |
IUSDAO.update(Registration registration,
IUS ius)
update.
|
void |
LaneDAO.update(Registration registration,
Lane lane)
update.
|
void |
ProcessingDAO.update(Registration registration,
Processing processing)
update.
|
void |
SampleDAO.update(Registration registration,
Sample sample)
update.
|
void |
SequencerRunDAO.update(Registration registration,
SequencerRun sequencerRun)
update.
|
void |
StudyDAO.update(Registration registration,
Study study)
update.
|
void |
WorkflowDAO.update(Registration registration,
Workflow workflow)
update.
|
void |
WorkflowParamDAO.update(Registration registration,
WorkflowParam workflowParam)
update.
|
void |
WorkflowParamValueDAO.update(Registration registration,
WorkflowParamValue workflowParamValue)
update.
|
void |
WorkflowRunDAO.update(Registration registration,
WorkflowRun workflowRun)
update.
|
void |
WorkflowRunParamDAO.update(Registration registration,
WorkflowRunParam workflowRunParam)
update.
|
Registration |
RegistrationDAO.updateDetached(Registration registration)
updateDetached.
|
Experiment |
ExperimentDAO.updateDetached(Registration registration,
Experiment experiment)
updateDetached.
|
File |
FileDAO.updateDetached(Registration registration,
File file)
updateDetached.
|
Invoice |
InvoiceDAO.updateDetached(Registration registration,
Invoice invoice)
updateDetached.
|
IUS |
IUSDAO.updateDetached(Registration registration,
IUS ius)
updateDetached.
|
Lane |
LaneDAO.updateDetached(Registration registration,
Lane lane)
updateDetached.
|
Processing |
ProcessingDAO.updateDetached(Registration registration,
Processing processing)
updateDetached.
|
Sample |
SampleDAO.updateDetached(Registration registration,
Sample sample)
updateDetached.
|
SequencerRun |
SequencerRunDAO.updateDetached(Registration registration,
SequencerRun sequencerRun)
updateDetached.
|
Study |
StudyDAO.updateDetached(Registration registration,
Study study)
updateDetached.
|
Workflow |
WorkflowDAO.updateDetached(Registration registration,
Workflow workflow)
updateDetached.
|
WorkflowParam |
WorkflowParamDAO.updateDetached(Registration registration,
WorkflowParam workflowParam)
updateDetached.
|
WorkflowParamValue |
WorkflowParamValueDAO.updateDetached(Registration registration,
WorkflowParamValue workflowParamValue)
updateDetached.
|
WorkflowRun |
WorkflowRunDAO.updateDetached(Registration registration,
WorkflowRun workflowRun)
updateDetached.
|
WorkflowRunParam |
WorkflowRunParamDAO.updateDetached(Registration registration,
WorkflowRunParam workflowRunParam)
updateDetached.
|
Modifier and Type | Method and Description |
---|---|
Registration |
RegistrationDAOHibernate.findByEmailAddress(String emailAddress)
findByEmailAddress.
|
Registration |
RegistrationDAOHibernate.findByEmailAddressAndPassword(String emailAddress,
String password)
findByEmailAddressAndPassword.
|
Registration |
RegistrationDAOHibernate.updateDetached(Registration registration)
updateDetached.
|
Modifier and Type | Method and Description |
---|---|
void |
RegistrationDAOHibernate.insert(Registration registration)
insert.
|
Integer |
ExperimentDAOHibernate.insert(Registration registration,
Experiment experiment)
insert.
|
Integer |
FileDAOHibernate.insert(Registration registration,
File file)
insert.
|
Integer |
InvoiceDAOHibernate.insert(Registration registration,
Invoice invoice)
insert.
|
Integer |
IUSDAOHibernate.insert(Registration registration,
IUS obj)
insert.
|
Integer |
LaneDAOHibernate.insert(Registration registration,
Lane lane)
insert.
|
Integer |
ProcessingDAOHibernate.insert(Registration registration,
Processing processing)
insert.
|
Integer |
SampleDAOHibernate.insert(Registration registration,
Sample sample)
insert.
|
Integer |
SequencerRunDAOHibernate.insert(Registration registration,
SequencerRun sequencerRun)
insert.
|
Integer |
SequencerRunDAOHibernate.insert(Registration registration,
SequencerRunWizardDTO sequencerRun)
insert.
|
Integer |
StudyDAOHibernate.insert(Registration registration,
Study study)
insert.
|
Integer |
WorkflowDAOHibernate.insert(Registration registration,
Workflow workflow)
insert.
|
Integer |
WorkflowParamDAOHibernate.insert(Registration registration,
WorkflowParam workflowParam)
insert.
|
Integer |
WorkflowParamValueDAOHibernate.insert(Registration registration,
WorkflowParamValue workflowParamValue)
insert.
|
Integer |
WorkflowRunDAOHibernate.insert(Registration registration,
WorkflowRun workflowRun)
insert.
|
void |
WorkflowRunParamDAOHibernate.insert(Registration registration,
WorkflowRunParam workflowRunParam)
insert.
|
void |
WorkflowRunParamDAOHibernate.insertFilesAsWorkflowRunParam(Registration registration,
WorkflowRun workflowRun,
Map<String,List<File>> files)
insertFilesAsWorkflowRunParam.
|
List<Platform> |
PlatformDAOHibernate.list(Registration registration)
list.
|
List<Workflow> |
WorkflowDAOHibernate.list(Registration registration)
list.
|
List<ExperimentLibraryDesign> |
ExperimentLibraryDesignDAOHibernate.list(Registration registration)
list.
|
List<Invoice> |
InvoiceDAOHibernate.list(Registration registration)
list.
|
List<Experiment> |
ExperimentDAOHibernate.list(Registration registration)
list.
|
List<Organism> |
OrganismDAOHibernate.list(Registration registration)
list.
|
List<LibraryStrategy> |
LibraryStrategyDAOHibernate.list(Registration registration)
list.
|
List<LibrarySource> |
LibrarySourceDAOHibernate.list(Registration registration)
list.
|
List<StudyType> |
StudyTypeDAOHibernate.list(Registration registration)
list.
|
List<LibrarySelection> |
LibrarySelectionDAOHibernate.list(Registration registration)
list.
|
List<WorkflowRun> |
WorkflowRunDAOHibernate.list(Registration registration,
Boolean isAsc)
list.
|
List<SequencerRun> |
SequencerRunDAOHibernate.list(Registration registration,
Boolean isAsc)
list.
|
List<Study> |
StudyDAOHibernate.list(Registration registration,
Boolean isAsc)
list.
|
List<Invoice> |
InvoiceDAOHibernate.list(Registration registration,
InvoiceState state)
list.
|
List<Workflow> |
WorkflowDAOHibernate.listMyShared(Registration registration)
listMyShared.
|
List<WorkflowRun> |
WorkflowRunDAOHibernate.listMyShared(Registration registration,
Boolean isAsc)
listMyShared.
|
List<Study> |
StudyDAOHibernate.listMyShared(Registration registration,
Boolean isAsc)
listMyShared.
|
List<Workflow> |
WorkflowRunDAOHibernate.listRelatedWorkflows(Registration registration)
listRelatedWorkflows.
|
List<WorkflowRun> |
WorkflowRunDAOHibernate.listRunning(Registration registration,
Boolean isAsc)
listRunning.
|
List<Sample> |
SampleDAOHibernate.listSample(Registration registaration)
listSample.
|
List<Workflow> |
WorkflowDAOHibernate.listSharedWithMe(Registration registration)
listSharedWithMe.
|
List<WorkflowRun> |
WorkflowRunDAOHibernate.listSharedWithMe(Registration registration,
Boolean isAsc)
listSharedWithMe.
|
List<Study> |
StudyDAOHibernate.listSharedWithMe(Registration registration,
Boolean isAsc)
listSharedWithMe.
|
List<Study> |
StudyDAOHibernate.listStudyHasFile(Registration registration,
String metaType,
Boolean isAsc)
listStudyHasFile.
|
File |
FileDAOHibernate.saveFile(org.springframework.web.multipart.MultipartFile uploadFile,
String folderStore,
Registration owner)
saveFile.
|
void |
RegistrationDAOHibernate.update(Registration registration)
update.
|
void |
ExperimentDAOHibernate.update(Registration registration,
Experiment experiment)
update.
|
void |
FileDAOHibernate.update(Registration registration,
File file)
update.
|
void |
InvoiceDAOHibernate.update(Registration registration,
Invoice invoice)
update.
|
void |
IUSDAOHibernate.update(Registration registration,
IUS ius)
update.
|
void |
LaneDAOHibernate.update(Registration registration,
Lane lane)
update.
|
void |
ProcessingDAOHibernate.update(Registration registration,
Processing processing)
update.
|
void |
SampleDAOHibernate.update(Registration registration,
Sample sample)
update.
|
void |
SequencerRunDAOHibernate.update(Registration registration,
SequencerRun sequencerRun)
update.
|
void |
StudyDAOHibernate.update(Registration registration,
Study study)
update.
|
void |
WorkflowDAOHibernate.update(Registration registration,
Workflow workflow)
update.
|
void |
WorkflowParamDAOHibernate.update(Registration registration,
WorkflowParam workflowParam)
update.
|
void |
WorkflowParamValueDAOHibernate.update(Registration registration,
WorkflowParamValue workflowParamValue)
update.
|
void |
WorkflowRunDAOHibernate.update(Registration registration,
WorkflowRun workflowRun)
update.
|
void |
WorkflowRunParamDAOHibernate.update(Registration registration,
WorkflowRunParam workflowRunParam)
update.
|
Registration |
RegistrationDAOHibernate.updateDetached(Registration registration)
updateDetached.
|
Experiment |
ExperimentDAOHibernate.updateDetached(Registration registration,
Experiment experiment)
updateDetached.
|
File |
FileDAOHibernate.updateDetached(Registration registration,
File file)
updateDetached.
|
Invoice |
InvoiceDAOHibernate.updateDetached(Registration registration,
Invoice invoice)
updateDetached.
|
IUS |
IUSDAOHibernate.updateDetached(Registration registration,
IUS ius)
updateDetached.
|
Lane |
LaneDAOHibernate.updateDetached(Registration registration,
Lane lane)
updateDetached.
|
Processing |
ProcessingDAOHibernate.updateDetached(Registration registration,
Processing processing)
updateDetached.
|
Sample |
SampleDAOHibernate.updateDetached(Registration registration,
Sample sample)
updateDetached.
|
SequencerRun |
SequencerRunDAOHibernate.updateDetached(Registration registration,
SequencerRun sequencerRun)
updateDetached.
|
Study |
StudyDAOHibernate.updateDetached(Registration registration,
Study study)
updateDetached.
|
Workflow |
WorkflowDAOHibernate.updateDetached(Registration registration,
Workflow workflow)
updateDetached.
|
WorkflowParam |
WorkflowParamDAOHibernate.updateDetached(Registration registration,
WorkflowParam workflowParam)
updateDetached.
|
WorkflowParamValue |
WorkflowParamValueDAOHibernate.updateDetached(Registration registration,
WorkflowParamValue workflowParamValue)
updateDetached.
|
WorkflowRun |
WorkflowRunDAOHibernate.updateDetached(Registration registration,
WorkflowRun workflowRun)
updateDetached.
|
WorkflowRunParam |
WorkflowRunParamDAOHibernate.updateDetached(Registration registration,
WorkflowRunParam workflowRunParam)
updateDetached.
|
Modifier and Type | Class and Description |
---|---|
class |
RegistrationDTO |
Modifier and Type | Method and Description |
---|---|
Registration |
SequencerRunWizardDTO.getDomainObject()
Getter for the field
domainObject . |
Registration |
RegistrationDTO.getDomainObject()
Getter for the field
domainObject . |
Registration |
Sample.getOwner()
Getter for the field
owner . |
Registration |
WorkflowRun.getOwner()
Getter for the field
owner . |
Registration |
File.getOwner()
Getter for the field
owner . |
Registration |
Workflow.getOwner()
Getter for the field
owner . |
Registration |
Lane.getOwner()
Getter for the field
owner . |
Registration |
IUS.getOwner()
Getter for the field
owner . |
Registration |
SequencerRun.getOwner()
Getter for the field
owner . |
Registration |
Experiment.getOwner()
Getter for the field
owner . |
Registration |
Invoice.getOwner()
Getter for the field
owner . |
Registration |
SequencerRunDTO.getOwner()
Getter for the field
owner . |
Registration |
Study.getOwner()
Getter for the field
owner . |
Registration |
Processing.getOwner()
Getter for the field
owner . |
Registration |
ShareWorkflowRun.getRegistration()
Getter for the field
registration . |
Registration |
ShareStudy.getRegistration()
Getter for the field
registration . |
Modifier and Type | Method and Description |
---|---|
int |
Registration.compareTo(Registration t) |
boolean |
Sample.givesPermissionInternal(Registration registration,
Set<Integer> considered)
Short-circuit permission checking by providing a set of entities that have already been checked
|
boolean |
WorkflowParam.givesPermissionInternal(Registration registration,
Set<Integer> considered)
Short-circuit permission checking by providing a set of entities that have already been checked
|
boolean |
Expense.givesPermissionInternal(Registration registration,
Set<Integer> considered)
Short-circuit permission checking by providing a set of entities that have already been checked
|
boolean |
WorkflowRun.givesPermissionInternal(Registration registration,
Set<Integer> considered)
Short-circuit permission checking by providing a set of entities that have already been checked
|
boolean |
File.givesPermissionInternal(Registration registration,
Set<Integer> considered) |
boolean |
Workflow.givesPermissionInternal(Registration registration,
Set<Integer> considered)
Short-circuit permission checking by providing a set of entities that have already been checked
|
boolean |
Lane.givesPermissionInternal(Registration registration,
Set<Integer> considered) |
boolean |
IUS.givesPermissionInternal(Registration registration,
Set<Integer> considered) |
boolean |
WorkflowRunParam.givesPermissionInternal(Registration registration,
Set<Integer> considered)
Short-circuit permission checking by providing a set of entities that have already been checked
|
boolean |
Registration.givesPermissionInternal(Registration registration,
Set<Integer> considered)
Short-circuit permission checking by providing a set of entities that have already been checked
|
boolean |
SequencerRun.givesPermissionInternal(Registration registration,
Set<Integer> considered)
Short-circuit permission checking by providing a set of entities that have already been checked
|
boolean |
Experiment.givesPermissionInternal(Registration registration,
Set<Integer> considered) |
boolean |
Invoice.givesPermissionInternal(Registration registration,
Set<Integer> considered) |
boolean |
WorkflowParamValue.givesPermissionInternal(Registration registration,
Set<Integer> considered)
Short-circuit permission checking by providing a set of entities that have already been checked
|
boolean |
Study.givesPermissionInternal(Registration registration,
Set<Integer> considered)
Short-circuit permission checking by providing a set of entities that have already been checked
|
boolean |
Processing.givesPermissionInternal(Registration registration,
Set<Integer> considered)
Short-circuit permission checking by providing a set of entities that have already been checked
|
void |
SequencerRunWizardDTO.setDomainObject(Registration domainObject)
Setter for the field
domainObject . |
void |
RegistrationDTO.setDomainObject(Registration domainObject)
Setter for the field
domainObject . |
void |
Sample.setOwner(Registration owner)
Setter for the field
owner . |
void |
WorkflowRun.setOwner(Registration owner)
Setter for the field
owner . |
void |
File.setOwner(Registration owner)
Setter for the field
owner . |
void |
Workflow.setOwner(Registration owner)
Setter for the field
owner . |
void |
Lane.setOwner(Registration owner)
Setter for the field
owner . |
void |
IUS.setOwner(Registration owner)
Setter for the field
owner . |
void |
SequencerRun.setOwner(Registration owner)
Setter for the field
owner . |
void |
Experiment.setOwner(Registration owner)
Setter for the field
owner . |
void |
Invoice.setOwner(Registration owner)
Setter for the field
owner . |
void |
SequencerRunDTO.setOwner(Registration owner)
Setter for the field
owner . |
void |
Study.setOwner(Registration owner)
Setter for the field
owner . |
void |
Processing.setOwner(Registration owner)
Setter for the field
owner . |
void |
ShareWorkflowRun.setRegistration(Registration registration)
Setter for the field
registration . |
void |
ShareStudy.setRegistration(Registration registration)
Setter for the field
registration . |
Modifier and Type | Method and Description |
---|---|
boolean |
PermissionsAware.givesPermission(Registration registration) |
boolean |
PermissionsAware.givesPermission(Registration registration,
Set<Integer> considered) |
abstract boolean |
PermissionsAware.givesPermissionInternal(Registration registration,
Set<Integer> considered)
Short-circuit permission checking by providing a set of entities that have already been checked
|
Modifier and Type | Field and Description |
---|---|
protected Registration |
BasicResource.registration |
protected Registration |
BasicRestlet.registration |
Modifier and Type | Method and Description |
---|---|
static Registration |
Security.getRegistration(javax.servlet.http.HttpServletRequest request)
getRegistration.
|
static Registration |
Security.requireRegistration(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response)
requireRegistration.
|
Modifier and Type | Method and Description |
---|---|
static String |
TreeNodeHtmlUtil.getAllHtml(Experiment experiment,
Registration registration,
Integer openingNodeId,
String treeType)
getAllHtml.
|
static String |
SequencerRunHtmlUtil.getAllHtml(IUS ius,
Registration registration,
String openingNodeId,
boolean isOpenProc,
boolean isVisibleProc,
String treeType)
getAllHtml.
|
static String |
StudyHtmlUtil.getAllHtml(IUS ius,
Registration registration,
String openingNodeId,
Integer currPosId,
List<String> listNodeId,
boolean isOpenProc,
boolean isVisibleProc,
String treeType)
getAllHtml.
|
static String |
TreeNodeHtmlUtil.getAllHtml(Lane lane,
Registration registration,
Integer openingNodeId,
String treeType)
getAllHtml.
|
static String |
SequencerRunHtmlUtil.getAllHtml(Lane lane,
Registration registration,
String openingNodeId,
String treeType)
getAllHtml.
|
static String |
SequencerRunHtmlUtil.getAllHtml(Processing processing,
Registration registration,
String openingNodeId,
Integer currPosId,
List<String> listNodeId,
boolean isFirstCall,
boolean isViewCurrentNode,
String treeType)
getAllHtml.
|
static String |
StudyHtmlUtil.getAllHtml(Processing processing,
Registration registration,
String openingNodeId,
Integer currPosId,
List<String> listNodeId,
boolean isFirstCall,
boolean isViewCurrentNode,
String treeType)
getAllHtml.
|
static String |
TreeNodeHtmlUtil.getAllHtml(Sample sample,
Registration registration,
Integer openingNodeId,
String treeType)
getAllHtml.
|
static String |
TreeNodeHtmlUtil.getAllHtml(Study study,
Registration registration,
String treeType)
getAllHtml.
|
static String |
NodeHtmlUtil.getAnalysisWorkflowHtml(WorkflowRun workflowRun,
Registration registration,
String typeTree,
boolean isOpen,
boolean isLast,
String treeType)
getAnalysisWorkflowHtml.
|
static String |
NodeHtmlUtil.getExperimentHtml(Experiment experiment,
Registration registration,
String typeTree,
String openingNodeId,
boolean isOpenProc,
String treeType)
getExperimentHtml.
|
static String |
SequencerRunHtmlUtil.getFileHtml(Processing proc,
Registration registration)
getFileHtml.
|
static String |
StudyHtmlUtil.getFileHtml(Processing proc,
Registration registration,
List<String> listStudyNodeId,
String treeType)
getFileHtml.
|
static String |
WorkflowRunHtmlUtil.getFileHtml(Processing proc,
WorkflowRun workflowRun,
Registration registration,
String typeTree)
getFileHtml.
|
static String |
SequencerRunHtmlUtil.getHtml(Object obj,
Registration registration,
List<String> listSeqencerRunNodeId,
String treeType)
getHtml.
|
static String |
StudyHtmlUtil.getHtml(Object obj,
Registration registration,
List<String> listStudyNodeId,
String treeType)
getHtml.
|
static String |
TreeNodeHtmlUtil.getHtml(Object obj,
Registration registration,
String treeType)
getHtml.
|
static String |
WorkflowRunHtmlUtil.getHtml(Processing processing,
WorkflowRun workflowRun,
Registration registration,
String typeTree,
List<String> listWorkflowNodeId,
String treeType)
getHtml.
|
static String |
WorkflowRunHtmlUtil.getHtml(Sample sample,
WorkflowRun workflowRun,
Registration registration,
String typeTree)
getHtml.
|
static String |
WorkflowRunHtmlUtil.getHtml(WorkflowRun workflowRun,
Registration registration,
String typeTree,
boolean isWorkflowRunWithSample,
String treeType)
getHtml.
|
static String |
NodeHtmlUtil.getIUSHtml(IUS ius,
Registration registration,
String typeTree,
String openingNodeId,
boolean isOpenProc,
boolean isVisibleProc,
String treeType)
getIUSHtml.
|
static String |
TreeNodeHtmlUtil.getLaneHtml(Lane lane,
Registration registration,
Integer openingNodeId)
getLaneHtml.
|
static String |
NodeHtmlUtil.getLaneHtml(Lane lane,
Registration registration,
String typeTree,
String openingNodeId,
String treeType)
getLaneHtml.
|
static String |
TreeNodeHtmlUtil.getNodeHtml(Processing processing,
Registration registration)
getNodeHtml.
|
static String |
NodeHtmlUtil.getNodeHtml(Processing processing,
Registration registration,
String typeTree,
boolean isOpenWfr,
boolean isOpenProc,
boolean isVisibleProc,
boolean isInnerWFR,
boolean isLastNode,
String treeType)
getNodeHtml.
|
static String |
NodeHtmlUtil.getProcessingHtml(Processing processing,
Registration registration,
String typeTree,
String openingNodeId,
String treeType)
getProcessingHtml.
|
static String |
TreeNodeHtmlUtil.getSampleHtml(Sample sample,
Registration registration,
Integer openingNodeId)
getSampleHtml.
|
static String |
NodeHtmlUtil.getSampleHtml(Sample sample,
Registration registration,
String typeTree,
String openingNodeId,
boolean isEnd,
boolean isOpenProc,
String treeType)
getSampleHtml.
|
static String |
NodeHtmlUtil.getSequencerRunHtml(SequencerRun sequencerRun,
Registration registration,
String openingNodeId,
String treeType)
getSequencerRunHtml.
|
static String |
TreeNodeHtmlUtil.getStydyHtml(Study study,
Registration registration,
Integer openingNodeId,
String treeType)
getStydyHtml.
|
static String |
NodeHtmlUtil.getStydyHtml(Study study,
Registration registration,
String openingNodeId,
boolean isOpenProc,
String treeType)
getStydyHtml.
|
static String |
NodeHtmlUtil.getWorkflowRunHtml(WorkflowRun workflowRun,
Registration registration,
String typeTree,
String openingNodeId,
String treeType)
getWorkflowRunHtml.
|
static String |
NodeHtmlUtil.getWorkflowRunHtmlWithIUSs(WorkflowRun workflowRun,
Registration registration,
String typeTree,
String openingNodeId,
String treeType)
getWorkflowRunHtmlWithIUSs.
|
Modifier and Type | Method and Description |
---|---|
void |
LoginController.DeleteTempFile(Registration registration)
DeleteTempFile.
|
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