StudyDAOHibernate (SeqWare 1.1.2 API)

java.lang.Object
- org.springframework.dao.support.DaoSupport
- - org.springframework.orm.hibernate3.support.HibernateDaoSupport
  - - net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

All Implemented Interfaces:

StudyDAO, org.springframework.beans.factory.InitializingBean
```
public class StudyDAOHibernate
extends org.springframework.orm.hibernate3.support.HibernateDaoSupport
implements StudyDAO
```
StudyDAOHibernate class.

Version:

$Id: $Id

Author:

boconnor

Field Summary
- Fields inherited from class org.springframework.dao.support.DaoSupport
  logger

Constructor Summary

Constructors
Constructor and Description

StudyDAOHibernate()
Constructor for StudyDAOHibernate.

Constructors
Constructor and Description
`StudyDAOHibernate()` Constructor for StudyDAOHibernate.

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`delete(Study study)` delete.
`List<Study>`	`findByCriteria(String criteria)` findByCriteria.
`List<Study>`	`findByCriteria(String criteria, boolean isCaseSens)` findByCriteria.
`Study`	`findByID(Integer expID)` findByID.
`List<Study>`	`findByOwnerID(Integer registrationId)` findByOwnerID.
`Study`	`findBySWAccession(Integer swAccession)` findBySWAccession.
`List<Study>`	`findByTitle(String title)` findByTitle.
`List<File>`	`getFiles(Integer studyId)` getFiles.
`List<File>`	`getFiles(Integer studyId, String metaType)` getFiles.
`int`	`getStatusCount(Study study, WorkflowRunStatus status)` Count the number of workflow runs with the given status, under the given study
`Integer`	`insert(Registration registration, Study study)` insert.
`Integer`	`insert(Study study)` insert.
`boolean`	`isHasFile(Integer studyId)` isHasFile.
`boolean`	`isHasFile(Integer studyId, String metaType)` isHasFile.
`List<Study>`	`list()` list.
`List<Study>`	`list(Registration registration, Boolean isAsc)` list.
`List<Study>`	`listMyShared(Registration registration, Boolean isAsc)` listMyShared.
`List<Study>`	`listSharedWithMe(Registration registration, Boolean isAsc)` listSharedWithMe.
`List<Study>`	`listStudyHasFile(Registration registration, String metaType, Boolean isAsc)` listStudyHasFile.
`void`	`merge(Study study)` merge.
`void`	`update(Registration registration, Study study)` update.
`void`	`update(Study study)` update.
`Study`	`updateDetached(Registration registration, Study study)` updateDetached.
`Study`	`updateDetached(Study study)` updateDetached.
`void`	`updateOwners(Integer swAccession)` updateOwners.

Methods inherited from class org.springframework.orm.hibernate3.support.HibernateDaoSupport
checkDaoConfig, convertHibernateAccessException, createHibernateTemplate, getHibernateTemplate, getSession, getSession, getSessionFactory, releaseSession, setHibernateTemplate, setSessionFactory

Methods inherited from class org.springframework.dao.support.DaoSupport
afterPropertiesSet, initDao

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - StudyDAOHibernate
```
public StudyDAOHibernate()
```
    Constructor for StudyDAOHibernate.
- Method Detail
  - insert
```
public Integer insert(Study study)
```
    insert.
    
    Specified by:
    
    insert in interface StudyDAO
    
    Parameters:
    study -
    
    Returns:
    a Integer object.
  - update
```
public void update(Study study)
```
    update.
    
    Specified by:
    
    update in interface StudyDAO
    
    Parameters:
    study -
  - merge
```
public void merge(Study study)
```
    merge.
    
    Specified by:
    
    merge in interface StudyDAO
    
    Parameters:
    study - a Study object.
  - delete
```
public void delete(Study study)
```
    delete.
    This deletion will result in just the study and experiments being deleted but the samples and IUS will remain. This will potentially cause orphans which is not really at all good. A better solution is to never delete but just use a deletion attribute.
    
    Specified by:
    
    delete in interface StudyDAO
    
    Parameters:
    study - a Study object.
  - list
```
public List<Study> list(Registration registration,
               Boolean isAsc)
```
    list.
    
    Specified by:
    
    list in interface StudyDAO
    
    Parameters:
    isAsc -
    registration - a Registration object.
    
    Returns:
    a List object.
  - list
```
public List<Study> list()
```
    list.
    
    Specified by:
    
    list in interface StudyDAO
    
    Returns:
    a List object.
  - listMyShared
```
public List<Study> listMyShared(Registration registration,
                       Boolean isAsc)
```
    listMyShared.
    
    Specified by:
    
    listMyShared in interface StudyDAO
    
    Parameters:
    isAsc -
    registration - a Registration object.
    
    Returns:
    a List object.
  - listSharedWithMe
```
public List<Study> listSharedWithMe(Registration registration,
                           Boolean isAsc)
```
    listSharedWithMe.
    
    Specified by:
    
    listSharedWithMe in interface StudyDAO
    
    Parameters:
    isAsc -
    registration - a Registration object.
    
    Returns:
    a List object.
  - getFiles
```
public List<File> getFiles(Integer studyId)
```
    getFiles.
    
    Specified by:
    
    getFiles in interface StudyDAO
    
    Parameters:
    studyId - a Integer object.
    
    Returns:
    a List object.
  - isHasFile
```
public boolean isHasFile(Integer studyId)
```
    isHasFile.
    
    Specified by:
    
    isHasFile in interface StudyDAO
    
    Parameters:
    studyId - a Integer object.
    
    Returns:
    a boolean.
  - getFiles
```
public List<File> getFiles(Integer studyId,
                  String metaType)
```
    getFiles.
    
    Specified by:
    
    getFiles in interface StudyDAO
    
    Parameters:
    studyId - a Integer object.
    metaType - a String object.
    
    Returns:
    a List object.
  - isHasFile
```
public boolean isHasFile(Integer studyId,
                String metaType)
```
    isHasFile.
    
    Specified by:
    
    isHasFile in interface StudyDAO
    
    Parameters:
    studyId - a Integer object.
    metaType - a String object.
    
    Returns:
    a boolean.
  - listStudyHasFile
```
public List<Study> listStudyHasFile(Registration registration,
                           String metaType,
                           Boolean isAsc)
```
    listStudyHasFile.
    
    Specified by:
    
    listStudyHasFile in interface StudyDAO
    
    Parameters:
    isAsc -
    registration - a Registration object.
    metaType - a String object.
    
    Returns:
    a List object.
  - findByTitle
```
public List<Study> findByTitle(String title)
```
    findByTitle.
    Finds an instance of Study in the database by the Study name.
    
    Specified by:
    
    findByTitle in interface StudyDAO
    
    Parameters:
    title - a String object.
    
    Returns:
    a Study object.
  - findByID
```
public Study findByID(Integer expID)
```
    findByID.
    Finds an instance of Study in the database by the Study ID.
    
    Specified by:
    
    findByID in interface StudyDAO
    
    Parameters:
    expID -
    
    Returns:
    a Study object.
  - findBySWAccession
```
public Study findBySWAccession(Integer swAccession)
```
    findBySWAccession.
    
    Specified by:
    
    findBySWAccession in interface StudyDAO
    
    Parameters:
    swAccession - a Integer object.
    
    Returns:
    a Study object.
  - findByOwnerID
```
public List<Study> findByOwnerID(Integer registrationId)
```
    findByOwnerID.
    
    Specified by:
    
    findByOwnerID in interface StudyDAO
    
    Parameters:
    registrationId - a Integer object.
    
    Returns:
    a List object.
  - findByCriteria
```
public List<Study> findByCriteria(String criteria,
                         boolean isCaseSens)
```
    findByCriteria.
    
    Specified by:
    
    findByCriteria in interface StudyDAO
    
    Parameters:
    criteria - a String object.
    isCaseSens - a boolean.
    
    Returns:
    a List object.
  - findByCriteria
```
public List<Study> findByCriteria(String criteria)
```
    findByCriteria.
    
    Specified by:
    
    findByCriteria in interface StudyDAO
    
    Parameters:
    criteria - a String object.
    
    Returns:
    a List object.
  - updateDetached
```
public Study updateDetached(Study study)
```
    updateDetached.
    
    Specified by:
    
    updateDetached in interface StudyDAO
    
    Parameters:
    study - a Study object.
    
    Returns:
    a Study object.
  - updateOwners
```
public void updateOwners(Integer swAccession)
```
    updateOwners.
    
    Specified by:
    
    updateOwners in interface StudyDAO
    
    Parameters:
    swAccession - a Integer object.
  - update
```
public void update(Registration registration,
          Study study)
```
    update.
    
    Specified by:
    
    update in interface StudyDAO
    
    Parameters:
    registration - a Registration object.
    study - a Study object.
  - insert
```
public Integer insert(Registration registration,
             Study study)
```
    insert.
    
    Specified by:
    
    insert in interface StudyDAO
    
    Parameters:
    study -
    registration - a Registration object.
    
    Returns:
    a Integer object.
  - updateDetached
```
public Study updateDetached(Registration registration,
                   Study study)
```
    updateDetached.
    
    Specified by:
    
    updateDetached in interface StudyDAO
    
    Parameters:
    registration - a Registration object.
    study - a Study object.
    
    Returns:
    a Study object.
  - getStatusCount
```
public int getStatusCount(Study study,
                 WorkflowRunStatus status)
```
    Count the number of workflow runs with the given status, under the given study
    
    Specified by:
    
    getStatusCount in interface StudyDAO
    
    Parameters:
    study - the study
    status - the status of the workflow runs to count
    
    Returns:
    the count

Class StudyDAOHibernate

Field Summary

Fields inherited from class org.springframework.dao.support.DaoSupport

Constructor Summary

Method Summary

Methods inherited from class org.springframework.orm.hibernate3.support.HibernateDaoSupport

Methods inherited from class org.springframework.dao.support.DaoSupport

Methods inherited from class java.lang.Object

Constructor Detail

StudyDAOHibernate

Method Detail

insert

update

merge

delete

list

list

listMyShared

listSharedWithMe

getFiles

isHasFile

getFiles

isHasFile

listStudyHasFile

findByTitle

findByID

findBySWAccession

findByOwnerID

findByCriteria

findByCriteria

updateDetached

updateOwners

update

insert

updateDetached

getStatusCount