Uses of Class
org.jbei.ice.storage.model.Entry

Packages that use Entry

Package	Description
org.jbei.ice.lib.access	Permissions related classes.
org.jbei.ice.lib.bulkupload
org.jbei.ice.lib.entry
org.jbei.ice.lib.entry.sequence
org.jbei.ice.lib.folder.collection
org.jbei.ice.lib.net
org.jbei.ice.lib.parsers	Parsers for different file formats.
org.jbei.ice.lib.parsers.sbol
org.jbei.ice.servlet
org.jbei.ice.storage	Database access classes.
org.jbei.ice.storage.hibernate.dao
org.jbei.ice.storage.model	Data models for ice objects.

Uses of Entry in org.jbei.ice.lib.access

Methods in org.jbei.ice.lib.access with parameters of type Entry

Modifier and Type	Method and Description
protected Permission	Permissions.addPermission(AccessPermission access, Entry entry, Folder folder, BulkUpload upload)
protected Permission	PermissionsController.addPermission(AccessPermission access, Entry entry, Folder folder, BulkUpload upload)
boolean	PermissionsController.isPubliclyVisible(Entry entry) Determines whether an entry has assigned public privileges either directly or by virtue of being in a folder that has public privileges assigned

Uses of Entry in org.jbei.ice.lib.bulkupload

Methods in org.jbei.ice.lib.bulkupload with parameters of type Entry

Modifier and Type	Method and Description
protected void	BulkEntryCreator.addWritePermission(Account account, Entry entry)
protected PartData	BulkEntryCreator.doUpdate(String userId, Entry entry, PartData data)
protected void	BulkEntryCreator.saveFiles(PartData data, Entry entry, HashMap<String,InputStream> files)
protected PartData	BulkUploadController.setFileData(String userId, Entry entry, PartData partData)
protected void	BulkUploadValidation.validateEntry(Entry entry)

Uses of Entry in org.jbei.ice.lib.entry

Methods in org.jbei.ice.lib.entry that return Entry

Modifier and Type	Method and Description
static Entry	EntryFactory.buildEntry(EntryType type)
Entry	EntryCreator.createEntry(Account account, Entry entry, ArrayList<AccessPermission> accessPermissions) Create an entry in the database.
protected Entry	HasEntry.getEntry(String id) Retrieve entry using a unique entry identifier

Methods in org.jbei.ice.lib.entry with parameters of type Entry

Modifier and Type	Method and Description
protected boolean	EntryLinks.addChildEntry(Entry child) Adds specified entry as a child of the entry associated with this
protected boolean	EntryLinks.addParentEntry(Entry parent)
protected void	EntryPermissionTask.addPermissions(Entry entry)
protected void	EntryCreator.addReadPermission(Account account, Group group, Entry entry)
protected void	EntryCreator.addWritePermission(Account account, Entry entry)
protected boolean	EntryController.canEdit(String userId, String depositor, Entry entry)
boolean	EntryAuthorization.canRead(String userId, Entry entry)
boolean	EntryAuthorization.canWrite(String userId, Entry entry) Determine if the referenced userId has write permissions for the entry.
Entry	EntryCreator.createEntry(Account account, Entry entry, ArrayList<AccessPermission> accessPermissions) Create an entry in the database.
static String	EntryUtil.entryFieldToValue(Entry entry, EntryField field)
protected static String	EntryUtil.getCommonFieldValues(Entry entry, EntryField field)
String	EntryAuthorization.getOwner(Entry entry)
protected void	EntryPermissionTask.removePermissions(Entry entry)
protected PartData	EntryController.retrieveEntryDetails(String userId, Entry entry)
void	EntryController.update(String userId, Entry entry)

Uses of Entry in org.jbei.ice.lib.entry.sequence

Methods in org.jbei.ice.lib.entry.sequence with parameters of type Entry

Modifier and Type	Method and Description
protected boolean	TraceSequences.canEdit(String userId, String depositor, Entry entry)
protected FeaturedDNASequence	SequenceController.getFeaturedSequence(Entry entry, boolean canEdit)
protected FeaturedDNASequence	PartSequence.getFeaturedSequence(Entry entry, boolean canEdit)
List<TraceSequence>	SequenceAnalysisController.getTraceSequences(Entry entry) Retrieve the TraceSequence associated with the given Entry entry.
void	SequenceAnalysisController.rebuildAllAlignments(Entry entry) Calculate sequence alignments between the sequence associated with an Entry entry with all the TraceSequences associated with that entry.

Uses of Entry in org.jbei.ice.lib.folder.collection

Methods in org.jbei.ice.lib.folder.collection with parameters of type Entry

Modifier and Type	Method and Description
protected PartData	Collection.setFileData(String userId, Entry entry, PartData partData)

Uses of Entry in org.jbei.ice.lib.net

Method parameters in org.jbei.ice.lib.net with type arguments of type Entry

Modifier and Type	Method and Description
protected void	RemoteEntriesAsCSV.writeLocalEntries(List<Entry> entries, List<EntryField> fields, com.opencsv.CSVWriter writer, ZipOutputStream zos)

Uses of Entry in org.jbei.ice.lib.parsers

Fields in org.jbei.ice.lib.parsers declared as Entry

Modifier and Type	Field and Description
protected Entry	AbstractParser.entry

Uses of Entry in org.jbei.ice.lib.parsers.sbol

Methods in org.jbei.ice.lib.parsers.sbol with parameters of type Entry

Modifier and Type	Method and Description
protected SequenceInfo	SBOLParser.parseToGenBank(org.sbolstandard.core2.SBOLDocument sbolDocument, String fileName, Entry entry, String uri) Parse the SBOL document to genbank format, save and associate with entry

Uses of Entry in org.jbei.ice.servlet

Methods in org.jbei.ice.servlet that return Entry

Modifier and Type	Method and Description
static Entry	InfoToModelFactory.infoToEntry(PartData info)
static Entry[]	InfoToModelFactory.infoToEntryForField(Entry entry, Entry plasmid, String value, EntryField field) Updates the entry based on the field that is specified.
protected static Entry	InfoToModelFactory.setPlasmidFields(PlasmidData plasmidData, Entry entry)
protected static Entry	InfoToModelFactory.setSeedFields(ArabidopsisSeedData seedData, Entry entry)
protected static Entry	InfoToModelFactory.setStrainFields(StrainData strainData, Entry entry)
static Entry	InfoToModelFactory.updateEntryField(PartData data, Entry entry) sets the corresponding fields in data only if they are not null

Methods in org.jbei.ice.servlet with parameters of type Entry

Modifier and Type	Method and Description
static Entry[]	InfoToModelFactory.infoToEntryForField(Entry entry, Entry plasmid, String value, EntryField field) Updates the entry based on the field that is specified.
protected static Entry	InfoToModelFactory.setPlasmidFields(PlasmidData plasmidData, Entry entry)
protected static Entry	InfoToModelFactory.setSeedFields(ArabidopsisSeedData seedData, Entry entry)
protected static Entry	InfoToModelFactory.setStrainFields(StrainData strainData, Entry entry)
static Entry	InfoToModelFactory.updateEntryField(PartData data, Entry entry) sets the corresponding fields in data only if they are not null

Uses of Entry in org.jbei.ice.storage

Methods in org.jbei.ice.storage with parameters of type Entry

Modifier and Type	Method and Description
static PartData	ModelToInfoFactory.createTableViewData(String userId, Entry entry, boolean includeOwnerInfo)
static PartData	ModelToInfoFactory.createTipView(Entry entry)
static PartData	ModelToInfoFactory.getCommon(PartData info, Entry entry)
static PartData	ModelToInfoFactory.getInfo(Entry entry)

Uses of Entry in org.jbei.ice.storage.hibernate.dao

Methods in org.jbei.ice.storage.hibernate.dao that return Entry

Modifier and Type	Method and Description
Entry	EntryDAO.create(Entry entry)
Entry	EntryDAO.get(long id) Retrieve an Entry object from the database by id.
Entry	EntryDAO.getByPartNumber(String partNumber) Retrieve an Entry by it's part number.
Entry	EntryDAO.getByRecordId(String recordId) Retrieve an Entry object in the database by recordId field.
protected Entry	EntryDAO.getEntryByField(String field, String fieldValue)

Methods in org.jbei.ice.storage.hibernate.dao that return types with arguments of type Entry

Modifier and Type	Method and Description
List<Entry>	ParameterDAO.filter(List<CustomField> fields)
List<Entry>	EntryDAO.getByName(String name) Retrieve an Entry by it's name.
List<Entry>	EntryDAO.getByVisibility(String ownerEmail, Visibility visibility, ColumnField field, boolean asc, int start, int limit, String filter)
List<Entry>	EntryDAO.getEntriesByIdSet(List<Long> ids) Retrieve Entry objects of the given list of ids.
List<Entry>	EntryDAO.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<Entry>	EntryDAO.retrieveAllEntries(ColumnField sort, boolean asc, int start, int limit, String filter)
List<Entry>	BulkUploadDAO.retrieveDraftEntries(long id, int start, int limit)
List<Entry>	FolderDAO.retrieveFolderContents(long folderId, PageParameters pageParameters, boolean visibleOnly) Retrieves list of entries that conforms to the parameters
List<Entry>	EntryDAO.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>	EntryDAO.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>	EntryDAO.retrieveVisibleEntries(Account account, Set<Group> groups, ColumnField sortField, boolean asc, int start, int count, String filter) Retrieve Entries visible to everyone.
List<Entry>	EntryDAO.sharedWithUserEntries(Account requester, Set<Group> accountGroups, ColumnField sort, boolean asc, int start, int limit, String filter)

Methods in org.jbei.ice.storage.hibernate.dao with parameters of type Entry

Modifier and Type	Method and Description
Entry	EntryDAO.create(Entry entry)
ShotgunSequence	ShotgunSequenceDAO.create(String fileName, String depositor, Entry entry, String fileUUID, Date date)
protected org.hibernate.query.Query<Permission>	PermissionDAO.createPermissionQuery(Entry entry, Folder folder, BulkUpload upload, Account account, Group group, boolean canRead, boolean canWrite)
int	AuditDAO.deleteAll(Entry entry)
void	EntryDAO.fullDelete(Entry entry)
void	EntryDAO.generateNextStrainNameForEntry(Entry entry, String prefix)
List<Audit>	AuditDAO.getAuditsForEntry(Entry entry, int limit, int offset, boolean asc, String sort)
int	AuditDAO.getAuditsForEntryCount(Entry entry)
List<Attachment>	AttachmentDAO.getByEntry(Entry entry) Retrieve all Attachments associated with the given Entry.
List<ShotgunSequence>	ShotgunSequenceDAO.getByEntry(Entry entry)
Sequence	SequenceDAO.getByEntry(Entry entry) Retrieve the Sequence object associated with the given Entry object.
List<TraceSequence>	TraceSequenceDAO.getByEntry(Entry entry, int start, int limit) Retrieve all TraceSequence objects associated with the given Entry object using the paging parameters, ordered by creation time in ascending order
int	CommentDAO.getCommentCount(Entry entry)
int	TraceSequenceDAO.getCountByEntry(Entry entry) Get number of trace sequences available for specified entry
List<Permission>	PermissionDAO.getEntryPermissions(Entry entry)
List<SequenceFeature>	SequenceFeatureDAO.getEntrySequenceFeatures(Entry entry)
int	SequenceFeatureDAO.getFeatureCount(Entry entry)
int	SampleDAO.getSampleCount(Entry entry)
List<Request>	RequestDAO.getSampleRequestByStatus(Account account, Entry entry, SampleRequestStatus status)
Request	RequestDAO.getSampleRequestInCart(Account account, Entry entry)
List<Sample>	SampleDAO.getSamplesByEntry(Entry entry)
String	SequenceDAO.getSequenceFilename(Entry entry)
Optional<String>	SequenceDAO.getSequenceString(Entry entry)
int	ShotgunSequenceDAO.getShotgunSequenceCount(Entry entry)
boolean	AttachmentDAO.hasAttachment(Entry entry)
boolean	PermissionDAO.hasPermission(Entry entry, Folder folder, BulkUpload upload, Account account, Group group, boolean canRead, boolean canWrite)
boolean	PermissionDAO.hasPermissionMulti(Entry entry, Set<Folder> folders, Account account, List<Group> groups, boolean canRead, boolean canWrite)
boolean	SampleDAO.hasSample(Entry entry)
int	PermissionDAO.removePermission(Entry entry, Folder folder, BulkUpload upload, Account account, Group group, boolean canRead, boolean canWrite)
List<Comment>	CommentDAO.retrieveComments(Entry entry)
Permission	PermissionDAO.retrievePermission(Entry entry, Folder folder, BulkUpload upload, Account account, Group group, boolean canRead, boolean canWrite)

Method parameters in org.jbei.ice.storage.hibernate.dao with type arguments of type Entry

Modifier and Type	Method and Description
Folder	FolderDAO.addFolderContents(Folder folder, List<Entry> entrys)
protected void	EntryDAO.checkAddFilter(List<javax.persistence.criteria.Predicate> predicates, javax.persistence.criteria.Root<Entry> root, String filter)

Uses of Entry in org.jbei.ice.storage.model

Subclasses of Entry in org.jbei.ice.storage.model

Modifier and Type	Class and Description
class	ArabidopsisSeed Store Arabidopsis Seed specific fields.
class	Part Store Part specific fields.
class	Plasmid Store Plasmid specific fields.
class	Strain Store Strain specific fields.

Methods in org.jbei.ice.storage.model that return Entry

Modifier and Type	Method and Description
Entry	Sequence.getEntry()
Entry	Comment.getEntry()
Entry	SelectionMarker.getEntry()
Entry	Request.getEntry()
Entry	ShotgunSequence.getEntry()
Entry	Permission.getEntry()
Entry	Link.getEntry()
Entry	Sample.getEntry()
Entry	Audit.getEntry()
Entry	Parameter.getEntry()
Entry	TraceSequence.getEntry()
Entry	Attachment.getEntry()

Methods in org.jbei.ice.storage.model that return types with arguments of type Entry

Modifier and Type	Method and Description
Set<Entry>	Folder.getContents()
Set<Entry>	BulkUpload.getContents()
Set<Entry>	Entry.getLinkedEntries()
Set<Entry>	Experiment.getSubjects()

Methods in org.jbei.ice.storage.model with parameters of type Entry

Modifier and Type	Method and Description
void	Sequence.setEntry(Entry entry)
void	Comment.setEntry(Entry entry)
void	SelectionMarker.setEntry(Entry entry)
void	Request.setEntry(Entry entry)
void	ShotgunSequence.setEntry(Entry entry)
void	Permission.setEntry(Entry entry)
void	Link.setEntry(Entry entry)
void	Sample.setEntry(Entry entry)
void	Audit.setEntry(Entry entry)
void	Parameter.setEntry(Entry entry)
void	TraceSequence.setEntry(Entry entry)
void	Attachment.setEntry(Entry entry)

Method parameters in org.jbei.ice.storage.model with type arguments of type Entry

Modifier and Type	Method and Description
void	BulkUpload.setContents(List<Entry> contents)
void	Experiment.setSubjects(Set<Entry> subjects)

Constructors in org.jbei.ice.storage.model with parameters of type Entry

Constructor and Description
Attachment(String description, String fileName, Entry entry) Attachment constructor.
Comment(Entry entry, Account account, String body)
SelectionMarker(String name, Entry entry)
Sequence(String sequence, String sequenceUser, String fwdHash, String revHash, Entry entry)
ShotgunSequence(Entry entry, String fileId, String filename, String depositor, Date creationTime)
TraceSequence(Entry entry, String fileId, String filename, String depositor, String sequence, Date creationTime)