| 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.hibernate |
Looks like utility classes for navigating the metadb.
|
| net.sourceforge.seqware.common.hibernate.reports |
A row of the workflow run report.
|
| net.sourceforge.seqware.common.metadata |
Critical classes that effectively convert API calls into actions against the DB and web service.
|
| net.sourceforge.seqware.common.model |
Hibernate model classes for the metadb.
|
| net.sourceforge.seqware.common.model.adapters |
Looks like converters from collections to XML.
|
| net.sourceforge.seqware.common.model.lists |
Looks like various container classes for XML serialization.
|
| net.sourceforge.seqware.webservice.resources.queries |
Report various things about the metadb.
|
| net.sourceforge.seqware.webservice.resources.tables |
More basic web resources.
|
| net.sourceforge.solexatools.util |
Portal stuff, to be assessed.
|
| net.sourceforge.solexatools.webapp.controller |
Portal stuff, to be assessed.
|
| net.sourceforge.solexatools.webapp.metamodel |
Portal stuff, to be assessed.
|
| Modifier and Type | Method and Description |
|---|---|
File |
FileService.findByID(Integer id)
findByID.
|
File |
FileService.findByPath(String path)
findByPath.
|
File |
FileService.findBySWAccession(Integer swAccession)
findBySWAccession.
|
File |
FileService.updateDetached(File file)
updateDetached.
|
File |
FileService.updateDetached(Registration registration,
File file)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<File> |
FileService.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<File> |
FileService.findByOwnerId(Integer registrationId)
findByOwnerId.
|
List<File> |
WorkflowRunService.findFiles(Integer swAccession)
findFiles.
|
List<File> |
LaneService.getFiles(Integer laneId)
getFiles.
|
List<File> |
ExperimentService.getFiles(Integer expId)
getFiles.
|
List<File> |
SampleService.getFiles(Integer sampleId)
getFiles.
|
List<File> |
StudyService.getFiles(Integer studyId)
getFiles.
|
List<File> |
FileService.getFiles(Integer fileId)
getFiles.
|
List<File> |
WorkflowRunService.getFiles(Integer wfrId)
getFiles.
|
List<File> |
ProcessingService.getFiles(Integer processingId)
getFiles.
|
List<File> |
IUSService.getFiles(Integer iusId)
getFiles.
|
List<File> |
LaneService.getFiles(Integer studyId,
String metaType)
getFiles.
|
List<File> |
ExperimentService.getFiles(Integer studyId,
String metaType)
getFiles.
|
List<File> |
SampleService.getFiles(Integer studyId,
String metaType)
getFiles.
|
List<File> |
StudyService.getFiles(Integer studyId,
String metaType)
getFiles.
|
List<File> |
FileService.getFiles(Integer fileId,
String metaType)
getFiles.
|
List<File> |
ProcessingService.getFiles(Integer processingId,
String metaType)
getFiles.
|
List<File> |
IUSService.getFiles(Integer iusId,
String metaType)
getFiles.
|
List<File> |
FileService.list()
list.
|
List<File> |
LaneService.listFile(Registration reqistration,
String typeNode,
List<File> list,
String[] ids,
String[] statuses)
listFile.
|
Set<File> |
FileService.setWithHasFile(Set<File> list,
String metaType)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
void |
FileService.delete(File file,
boolean deleteRealFiles)
delete.
|
Integer |
FileService.insert(File file)
insert.
|
Integer |
FileService.insert(Registration registration,
File file)
insert.
|
void |
FileService.update(File file)
update.
|
void |
FileService.update(Registration registration,
File file)
update.
|
File |
FileService.updateDetached(File file)
updateDetached.
|
File |
FileService.updateDetached(Registration registration,
File file)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
void |
FileService.deleteAll(List<File> file,
boolean deleteRealFiles)
deleteAll.
|
Integer |
WorkflowRunService.insert(Registration registration,
WorkflowRun workflowRun,
SortedSet<WorkflowRunParam> workflowRunParams,
Map<String,List<File>> allSelectedFiles)
insert.
|
Integer |
WorkflowRunService.insert(WorkflowRun workflowRun,
SortedSet<WorkflowRunParam> workflowRunParams,
Map<String,List<File>> allSelectedFiles)
insert.
|
List<File> |
LaneService.listFile(Registration reqistration,
String typeNode,
List<File> list,
String[] ids,
String[] statuses)
listFile.
|
Set<File> |
FileService.setWithHasFile(Set<File> list,
String metaType)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
File |
FileServiceImpl.findByID(Integer fileId)
findByID.
|
File |
FileServiceImpl.findByPath(String path)
findByPath.
|
File |
FileServiceImpl.findBySWAccession(Integer swAccession)
findBySWAccession.
|
File |
FileServiceImpl.updateDetached(File file)
updateDetached.
|
File |
FileServiceImpl.updateDetached(Registration registration,
File file)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<File> |
FileServiceImpl.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<File> |
FileServiceImpl.findByOwnerId(Integer registrationId)
findByOwnerId.
|
List<File> |
WorkflowRunServiceImpl.findFiles(Integer swAccession)
findFiles.
|
List<File> |
StudyServiceImpl.getFiles(Integer studyId)
getFiles.
|
List<File> |
WorkflowRunServiceImpl.getFiles(Integer wfrId)
getFiles.
|
List<File> |
ExperimentServiceImpl.getFiles(Integer experimentId)
getFiles.
|
List<File> |
LaneServiceImpl.getFiles(Integer laneId)
getFiles.
|
List<File> |
SampleServiceImpl.getFiles(Integer sampleId)
getFiles.
|
List<File> |
ProcessingServiceImpl.getFiles(Integer processingId)
getFiles.
|
List<File> |
IUSServiceImpl.getFiles(Integer iusId)
getFiles.
|
List<File> |
FileServiceImpl.getFiles(Integer fileId)
getFiles.
|
List<File> |
StudyServiceImpl.getFiles(Integer studyId,
String metaType)
getFiles.
|
List<File> |
ExperimentServiceImpl.getFiles(Integer studyId,
String metaType)
getFiles.
|
List<File> |
LaneServiceImpl.getFiles(Integer studyId,
String metaType)
getFiles.
|
List<File> |
SampleServiceImpl.getFiles(Integer studyId,
String metaType)
getFiles.
|
List<File> |
ProcessingServiceImpl.getFiles(Integer processingId,
String metaType)
getFiles.
|
List<File> |
IUSServiceImpl.getFiles(Integer iusId,
String metaType)
getFiles.
|
List<File> |
FileServiceImpl.getFiles(Integer fileId,
String metaType)
getFiles.
|
List<File> |
FileServiceImpl.list()
list.
|
List<File> |
LaneServiceImpl.listFile(Registration reqistration,
String typeNode,
List<File> list,
String[] ids,
String[] statuses)
listFile.
|
Set<File> |
FileServiceImpl.setWithHasFile(Set<File> list,
String metaType)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
void |
FileServiceImpl.delete(File file,
boolean deleteRealFiles)
delete.
|
Integer |
FileServiceImpl.insert(File file)
insert.
|
Integer |
FileServiceImpl.insert(Registration registration,
File file)
insert.
|
void |
FileServiceImpl.update(File file)
update.
|
void |
FileServiceImpl.update(Registration registration,
File file)
update.
|
File |
FileServiceImpl.updateDetached(File file)
updateDetached.
|
File |
FileServiceImpl.updateDetached(Registration registration,
File file)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
void |
FileServiceImpl.deleteAll(List<File> files,
boolean deleteRealFiles)
deleteAll.
|
Integer |
WorkflowRunServiceImpl.insert(Registration registration,
WorkflowRun workflowRun,
SortedSet<WorkflowRunParam> workflowRunParams,
Map<String,List<File>> allSelectedFiles)
insert.
|
Integer |
WorkflowRunServiceImpl.insert(WorkflowRun workflowRun,
SortedSet<WorkflowRunParam> workflowRunParams,
Map<String,List<File>> allSelectedFiles)
insert.
|
List<File> |
LaneServiceImpl.listFile(Registration reqistration,
String typeNode,
List<File> list,
String[] ids,
String[] statuses)
listFile.
|
Set<File> |
FileServiceImpl.setWithHasFile(Set<File> list,
String metaType)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
File |
FileDAO.findByID(Integer id)
findByID.
|
File |
FileDAO.findByPath(String path)
findByPath.
|
File |
FileDAO.findBySWAccession(Integer swAccession)
findBySWAccession.
|
File |
FileDAO.updateDetached(File file)
updateDetached.
|
File |
FileDAO.updateDetached(Registration registration,
File file)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<File> |
FileDAO.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<File> |
FileDAO.findByOwnerId(Integer registrationId)
findByOwnerId.
|
List<File> |
IUSDAO.getFiles(Integer iusId)
getFiles.
|
List<File> |
ExperimentDAO.getFiles(Integer experimentId)
getFiles.
|
List<File> |
ProcessingDAO.getFiles(Integer processingId)
getFiles.
|
List<File> |
StudyDAO.getFiles(Integer studyId)
getFiles.
|
List<File> |
SampleDAO.getFiles(Integer sampleId)
getFiles.
|
List<File> |
LaneDAO.getFiles(Integer laneId)
getFiles.
|
List<File> |
IUSDAO.getFiles(Integer iusId,
String metaType)
getFiles.
|
List<File> |
ExperimentDAO.getFiles(Integer expId,
String metaType)
getFiles.
|
List<File> |
ProcessingDAO.getFiles(Integer processingId,
String metaType)
getFiles.
|
List<File> |
StudyDAO.getFiles(Integer studyId,
String metaType)
getFiles.
|
List<File> |
SampleDAO.getFiles(Integer sampleId,
String metaType)
getFiles.
|
List<File> |
LaneDAO.getFiles(Integer studyId,
String metaType)
getFiles.
|
List<File> |
FileDAO.list()
list.
|
| Modifier and Type | Method and Description |
|---|---|
void |
FileDAO.delete(File file)
delete.
|
List<FileAttribute> |
FileAttributeDAO.get(File file)
get.
|
Integer |
FileDAO.insert(File file)
insert.
|
Integer |
FileDAO.insert(Registration registration,
File file)
insert.
|
void |
FileDAO.update(File file)
update.
|
void |
FileDAO.update(Registration registration,
File file)
update.
|
File |
FileDAO.updateDetached(File file)
updateDetached.
|
File |
FileDAO.updateDetached(Registration registration,
File file)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
void |
FileDAO.deleteAll(List<File> files)
deleteAll.
|
void |
FileDAO.deleteAllWithFolderStore(List<File> list)
deleteAllWithFolderStore.
|
void |
WorkflowRunParamDAO.insertFilesAsWorkflowRunParam(Registration registration,
WorkflowRun workflowRun,
Map<String,List<File>> files)
insertFilesAsWorkflowRunParam.
|
void |
WorkflowRunParamDAO.insertFilesAsWorkflowRunParam(WorkflowRun workflowRun,
Map<String,List<File>> files)
insertFilesAsWorkflowRunParam.
|
| Modifier and Type | Method and Description |
|---|---|
File |
FileDAOHibernate.findByID(Integer id)
findByID.
|
File |
FileDAOHibernate.findByPath(String path)
findByPath.
|
File |
FileDAOHibernate.findBySWAccession(Integer swAccession)
findBySWAccession.
|
File |
FileDAOHibernate.updateDetached(File file)
updateDetached.
|
File |
FileDAOHibernate.updateDetached(Registration registration,
File file)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<File> |
FileDAOHibernate.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<File> |
FileDAOHibernate.findByOwnerId(Integer registrationId)
findByOwnerId.
|
List<File> |
SampleDAOHibernate.getFiles(Integer sampleId)
getFiles.
|
List<File> |
StudyDAOHibernate.getFiles(Integer studyId)
getFiles.
|
List<File> |
ExperimentDAOHibernate.getFiles(Integer experimentId)
getFiles.
|
List<File> |
LaneDAOHibernate.getFiles(Integer laneId)
getFiles.
|
List<File> |
IUSDAOHibernate.getFiles(Integer iusId)
getFiles.
|
List<File> |
ProcessingDAOHibernate.getFiles(Integer processingId)
getFiles.
|
List<File> |
SampleDAOHibernate.getFiles(Integer sampleId,
String metaType)
getFiles.
|
List<File> |
StudyDAOHibernate.getFiles(Integer studyId,
String metaType)
getFiles.
|
List<File> |
ExperimentDAOHibernate.getFiles(Integer experimentId,
String metaType)
getFiles.
|
List<File> |
LaneDAOHibernate.getFiles(Integer laneId,
String metaType)
getFiles.
|
List<File> |
IUSDAOHibernate.getFiles(Integer iusId,
String metaType)
getFiles.
|
List<File> |
ProcessingDAOHibernate.getFiles(Integer processingId,
String metaType)
getFiles.
|
List<File> |
FileDAOHibernate.list()
list.
|
| Modifier and Type | Method and Description |
|---|---|
void |
FileDAOHibernate.delete(File file)
delete.
|
List<FileAttribute> |
FileAttributeDAOHibernate.get(File file)
get.
|
Integer |
FileDAOHibernate.insert(File file)
insert.
|
Integer |
FileDAOHibernate.insert(Registration registration,
File file)
insert.
|
void |
FileDAOHibernate.update(File file)
update.
|
void |
FileDAOHibernate.update(Registration registration,
File file)
update.
|
File |
FileDAOHibernate.updateDetached(File file)
updateDetached.
|
File |
FileDAOHibernate.updateDetached(Registration registration,
File file)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
void |
FileDAOHibernate.deleteAll(List<File> files)
deleteAll.
|
void |
FileDAOHibernate.deleteAllWithFolderStore(List<File> list)
deleteAllWithFolderStore.
|
void |
WorkflowRunParamDAOHibernate.insertFilesAsWorkflowRunParam(Registration registration,
WorkflowRun workflowRun,
Map<String,List<File>> files)
insertFilesAsWorkflowRunParam.
|
void |
WorkflowRunParamDAOHibernate.insertFilesAsWorkflowRunParam(WorkflowRun workflowRun,
Map<String,List<File>> paramNameFileHash)
insertFilesAsWorkflowRunParam.
|
| Modifier and Type | Method and Description |
|---|---|
protected Collection<File> |
WorkflowRunReport.findFiles(Collection<Processing> processings) |
| Modifier and Type | Method and Description |
|---|---|
Collection<File> |
WorkflowRunReportRow.getAllInputFiles()
Getter for the field
allInputFiles. |
Collection<File> |
WorkflowRunReportRow.getImmediateInputFiles()
Getter for the field
immediateInputFiles. |
Collection<File> |
WorkflowRunReportRow.getOutputFiles()
Getter for the field
outputFiles. |
| Modifier and Type | Method and Description |
|---|---|
void |
WorkflowRunReportRow.setAllInputFiles(Collection<File> allInputFiles)
Setter for the field
allInputFiles. |
void |
WorkflowRunReportRow.setImmediateInputFiles(Collection<File> immediateInputFiles)
Setter for the field
immediateInputFiles. |
void |
WorkflowRunReportRow.setOutputFiles(Collection<File> outputFiles)
Setter for the field
outputFiles. |
| Modifier and Type | Method and Description |
|---|---|
File |
MetadataWS.LowLevel.existsFile(String searchString) |
File |
MetadataWS.getFile(int swAccession)
getFile.
|
File |
Metadata.getFile(int swAccession)
getFile.
|
File |
MetadataNoConnection.getFile(int swAccession)
getFile.
|
File |
MetadataDB.getFile(int swAccession)
getFile.
|
File |
MetadataInMemory.getFile(int swAccession) |
| Modifier and Type | Method and Description |
|---|---|
File |
FileAttribute.getFile()
Getter for the field
file. |
File |
FileReportRow.getFile()
Getter for the field
file. |
| Modifier and Type | Method and Description |
|---|---|
List<File> |
WorkflowParam.getFiles()
Getter for the field
files. |
Set<File> |
Processing.getFiles()
Getter for the field
files. |
| Modifier and Type | Method and Description |
|---|---|
int |
File.compareTo(File that) |
void |
FileAttribute.setAttributeParent(File parent) |
void |
FileAttribute.setFile(File file)
Setter for the field
file. |
void |
FileReportRow.setFile(File file)
Setter for the field
file. |
| Modifier and Type | Method and Description |
|---|---|
void |
WorkflowParam.setFiles(List<File> files)
Setter for the field
files. |
void |
Processing.setFiles(Set<File> files)
Setter for the field
files. |
| Modifier and Type | Method and Description |
|---|---|
Set<File> |
XmlizeFileSet.unmarshal(FileList vt) |
| Modifier and Type | Method and Description |
|---|---|
FileList |
XmlizeFileSet.marshal(Set<File> bt) |
| Modifier and Type | Field and Description |
|---|---|
protected List<File> |
FileList.tList |
| Modifier and Type | Method and Description |
|---|---|
List<File> |
FileList.getList()
getList.
|
| Modifier and Type | Method and Description |
|---|---|
void |
FileList.add(File ex)
add.
|
| Modifier and Type | Method and Description |
|---|---|
void |
FileList.setList(List<File> list)
setList.
|
| Modifier and Type | Method and Description |
|---|---|
List<File> |
WorkflowRunIdFilesResource.hello(int wrSWA)
hello.
|
| Modifier and Type | Method and Description |
|---|---|
protected WorkflowRunList2 |
FileChildWorkflowRunsResource.handleWorkflowRunsViaChild(Set<File> files,
net.sf.beanlib.hibernate3.Hibernate3DtoCopier copier) |
protected WorkflowRunList2 |
FileChildWorkflowRunsResource.handleWorkflowRunsViaIUS(Set<File> files,
net.sf.beanlib.hibernate3.Hibernate3DtoCopier copier) |
protected WorkflowRunList2 |
FileChildWorkflowRunsResource.handleWorkflowRunsViaLane(Set<File> files,
net.sf.beanlib.hibernate3.Hibernate3DtoCopier copier) |
| Modifier and Type | Method and Description |
|---|---|
static Map<String,List<File>> |
LaunchWorkflowUtil.getAllSelectedFiles(javax.servlet.http.HttpServletRequest request)
Get all selected Files, the files are organized by the name of the parameter (key) and a list of files selected (value) via a hash.
|
static List<File> |
LaunchWorkflowUtil.getCurrentSelectedFiles(javax.servlet.http.HttpServletRequest request)
getCurrentSelectedFiles.
|
List<File> |
SummaryLine.getFiles()
Getter for the field
files. |
static List<File> |
BulkUtil.getFiles(javax.servlet.http.HttpServletRequest request,
String nameList)
getFiles.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
LaunchWorkflowUtil.setCurrentSelectedFiles(javax.servlet.http.HttpServletRequest request,
List<File> selectedFilesOneParam)
setCurrentSelectedFiles.
|
void |
SummaryLine.setFiles(List<File> files)
Setter for the field
files. |
| Modifier and Type | Method and Description |
|---|---|
org.springframework.web.servlet.ModelAndView |
FileController.handleDelete(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
File command)
Handles the user's request to delete their file.
|
| Modifier and Type | Method and Description |
|---|---|
File |
StudySampleReportFileLineItem.getFile()
Getter for the field
file. |
| Modifier and Type | Method and Description |
|---|---|
void |
StudySampleReportFileLineItem.setFile(File file)
Setter for the field
file. |
| Constructor and Description |
|---|
StudySampleReportFileLineItem(Sample root,
Sample child,
IUS ius,
File file)
Constructor for StudySampleReportFileLineItem.
|
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