org.jbei.ice.storage.hibernate.dao

Class EntryDAO

java.lang.Object

org.jbei.ice.storage.hibernate.HibernateRepository<Entry>

org.jbei.ice.storage.hibernate.dao.EntryDAO

All Implemented Interfaces:

IRepository<Entry>

public class EntryDAO
extends HibernateRepository<Entry>

DAO to manipulate Entry objects in the database.

Author:

Hector Plahar

Constructor Summary

Constructors

Constructor and Description
EntryDAO()

Method Summary

Modifier and Type	Method and Description
protected void	checkAddFilter(List<javax.persistence.criteria.Predicate> predicates, javax.persistence.criteria.Root<Entry> root, String filter)
protected String	columnFieldToString(ColumnField field)
Entry	create(Entry entry) Creates new object in the database
List<Long>	filterByUserId(String userId, List<Long> entries)
void	fullDelete(Entry entry)
void	generateNextStrainNameForEntry(Entry entry, String prefix)
Entry	get(long id) Retrieve an Entry object from the database by id.
long	getAllEntryCount(String filter)
List<Entry>	getByName(String name) Retrieve an Entry by it's name.
Entry	getByPartNumber(String partNumber) Retrieve an Entry by it's part number.
Entry	getByRecordId(String recordId) Retrieve an Entry object in the database by recordId field.
List<Entry>	getByVisibility(String ownerEmail, Visibility visibility, ColumnField field, boolean asc, int start, int limit, String filter)
long	getByVisibilityCount(String ownerEmail, Visibility visibility, String filter)
long	getByVisibilityCount(Visibility visibility)
int	getDeletedCount(String ownerUserId)
List<Entry>	getEntriesByIdSet(List<Long> ids) Retrieve Entry objects of the given list of ids.
protected Entry	getEntryByField(String field, String fieldValue)
String	getEntrySummary(long id)
List<String>	getMatchingEntryPartNumbers(String token, int limit, Set<String> include)
List<String>	getMatchingPlasmidField(AutoCompleteField field, String token, int limit)
List<Long>	getOwnerEntryIds(String ownerEmail, EntryType type) Retrieves list of entry ids whose owner email column matches the specified ownerEmail parameter, with a visibility of
List<Entry>	getParents(long entryId) links are stored in a join table in the form [entry_id, linked_entry_id] which is used to represent a parent child reln.
List<String>	getRecordTypes(List<Long> list)
List<Long>	getVisibleEntryIds(boolean admin, Group publicGroup)
long	ownerEntryCount(Account requester, String ownerEmail, Set<Group> accountGroups)
long	ownerEntryCount(String ownerEmail)
List<Entry>	retrieveAllEntries(ColumnField sort, boolean asc, int start, int limit, String filter)
List<Entry>	retrieveOwnerEntries(String ownerEmail, ColumnField sort, boolean asc, int start, int limit, String filter) Retrieves entries owned by account with specified email and with visibility of "pending" or "ok"
List<Entry>	retrieveUserEntries(Account requester, String owner, Set<Group> requesterGroups, ColumnField sortField, boolean asc, int start, int limit, String filter) Retrieves the entries for the specified owner, that the requester has read access to
List<Entry>	retrieveVisibleEntries(Account account, Set<Group> groups, ColumnField sortField, boolean asc, int start, int count, String filter) Retrieve Entries visible to everyone.
int	setEntryVisibility(List<Long> list, Visibility ok)
long	sharedEntryCount(Account requester, Set<Group> accountGroups, String filter) An entry is shared if requester has explicit read or write permissions of belongs to a group that have explicit read or write permissions
List<Entry>	sharedWithUserEntries(Account requester, Set<Group> accountGroups, ColumnField sort, boolean asc, int start, int limit, String filter)
List<Long>	sharedWithUserEntryIds(Account account, Set<Group> groups)
long	visibleEntryCount(Account account, Set<Group> groups, String filter)

Methods inherited from class org.jbei.ice.storage.hibernate.HibernateRepository

currentSession, delete, get, getBuilder, update

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

EntryDAO

public EntryDAO()

Method Detail

get

public Entry get(long id)

Retrieve an Entry object from the database by id.

Parameters:

id - unique local identifier for entry record (typically synthetic database id)

Returns:

Entry entry record associated with id

Throws:

DAOException

getEntrySummary

public String getEntrySummary(long id)

getMatchingPlasmidField

public List<String> getMatchingPlasmidField(AutoCompleteField field,
                                            String token,
                                            int limit)

getMatchingEntryPartNumbers

public List<String> getMatchingEntryPartNumbers(String token,
                                                int limit,
                                                Set<String> include)

getEntryByField

protected Entry getEntryByField(String field,
                                String fieldValue)

getByRecordId

public Entry getByRecordId(String recordId)

Retrieve an Entry object in the database by recordId field.

Parameters:

recordId - unique global identifier for entry record (typically UUID)

Returns:

Entry entry record associated with recordId

Throws:

DAOException

getByPartNumber

public Entry getByPartNumber(String partNumber)

Retrieve an Entry by it's part number.

If multiple Entries exist with the same part number, this method throws an exception.

Parameters:

partNumber - part number associated with entry

Returns:

Entry

Throws:

DAOException

getByName

public List<Entry> getByName(String name)

Retrieve an Entry by it's name. Note that name is not a unique field so this could return more than one entry

Parameters:

name - name associated with entry

Returns:

Entry.

Throws:

DAOException - on hibernate exception

retrieveVisibleEntries

public List<Entry> retrieveVisibleEntries(Account account,
                                          Set<Group> groups,
                                          ColumnField sortField,
                                          boolean asc,
                                          int start,
                                          int count,
                                          String filter)

Retrieve Entries visible to everyone.

Returns:

Number of visible entries.

Throws:

DAOException - on hibernate exception

visibleEntryCount

public long visibleEntryCount(Account account,
                              Set<Group> groups,
                              String filter)

checkAddFilter

protected void checkAddFilter(List<javax.persistence.criteria.Predicate> predicates,
                              javax.persistence.criteria.Root<Entry> root,
                              String filter)

sharedEntryCount

public long sharedEntryCount(Account requester,
                             Set<Group> accountGroups,
                             String filter)

An entry is shared if requester has explicit read or write permissions of belongs to a group that have explicit read or write permissions

Parameters:

requester - account that entries are shared with

accountGroups - groups that account belongs to

Returns:

number of entries that have been shared with user

sharedWithUserEntries

public List<Entry> sharedWithUserEntries(Account requester,
                                         Set<Group> accountGroups,
                                         ColumnField sort,
                                         boolean asc,
                                         int start,
                                         int limit,
                                         String filter)

sharedWithUserEntryIds

public List<Long> sharedWithUserEntryIds(Account account,
                                         Set<Group> groups)

retrieveUserEntries

public List<Entry> retrieveUserEntries(Account requester,
                                       String owner,
                                       Set<Group> requesterGroups,
                                       ColumnField sortField,
                                       boolean asc,
                                       int start,
                                       int limit,
                                       String filter)

Retrieves the entries for the specified owner, that the requester has read access to

Parameters:

requester - account for user making request

owner - user id of entries' owner

requesterGroups - groups that the requester is a member of. Used to check access permissions

sortField - field for sort

asc - sort order

start - index to start retrieving records from

limit - maximum number of entries to retrieve

Returns:

list of entries matching specified criteria

Throws:

DAOException - on HibernateException

getEntriesByIdSet

public List<Entry> getEntriesByIdSet(List<Long> ids)

Retrieve Entry objects of the given list of ids.

Parameters:

ids - list of ids to retrieve

Returns:

ArrayList of Entry objects.

Throws:

DAOException

create

public Entry create(Entry entry)

Description copied from class: HibernateRepository

Creates new object in the database

Specified by:

create in interface IRepository<Entry>

Overrides:

create in class HibernateRepository<Entry>

Parameters:

entry - DataModel object to create

Returns:

Object created DataModel object

generateNextStrainNameForEntry

public void generateNextStrainNameForEntry(Entry entry,
                                           String prefix)

getByVisibility

public List<Entry> getByVisibility(String ownerEmail,
                                   Visibility visibility,
                                   ColumnField field,
                                   boolean asc,
                                   int start,
                                   int limit,
                                   String filter)

getByVisibilityCount

public long getByVisibilityCount(String ownerEmail,
                                 Visibility visibility,
                                 String filter)

getByVisibilityCount

public long getByVisibilityCount(Visibility visibility)

columnFieldToString

protected String columnFieldToString(ColumnField field)

retrieveOwnerEntries

public List<Entry> retrieveOwnerEntries(String ownerEmail,
                                        ColumnField sort,
                                        boolean asc,
                                        int start,
                                        int limit,
                                        String filter)

Retrieves entries owned by account with specified email and with visibility of "pending" or "ok"

Parameters:

ownerEmail - email for account whose entries are to be retrieved

sort - field to sort results on

asc - sort order

start - start of retrieve

limit - maximum number of records to retrieve from

filter - filter for entries

Returns:

list of matching entries

Throws:

DAOException - on Hibernate Exception

getOwnerEntryIds

public List<Long> getOwnerEntryIds(String ownerEmail,
                                   EntryType type)

Retrieves list of entry ids whose owner email column matches the specified ownerEmail parameter, with a visibility of

OK

or

PENDING

and if not null, matches the type

Parameters:

ownerEmail - value of owner email column that desired entries must match

type - option entry type parameter

Returns:

list of ids for all matching entries

getVisibleEntryIds

public List<Long> getVisibleEntryIds(boolean admin,
                                     Group publicGroup)

getAllEntryCount

public long getAllEntryCount(String filter)

Returns:

number of entries that have visibility of "OK"

retrieveAllEntries

public List<Entry> retrieveAllEntries(ColumnField sort,
                                      boolean asc,
                                      int start,
                                      int limit,
                                      String filter)

ownerEntryCount

public long ownerEntryCount(String ownerEmail)

ownerEntryCount

public long ownerEntryCount(Account requester,
                            String ownerEmail,
                            Set<Group> accountGroups)

fullDelete

public void fullDelete(Entry entry)

getParents

public List<Entry> getParents(long entryId)

links are stored in a join table in the form [entry_id, linked_entry_id] which is used to represent a parent child reln. This method returns the parents in the reln

getDeletedCount

public int getDeletedCount(String ownerUserId)

setEntryVisibility

public int setEntryVisibility(List<Long> list,
                              Visibility ok)

getRecordTypes

public List<String> getRecordTypes(List<Long> list)

filterByUserId

public List<Long> filterByUserId(String userId,
                                 List<Long> entries)