org.jbei.ice.storage.model

Class Entry

java.lang.Object

org.jbei.ice.storage.model.Entry

All Implemented Interfaces:

DataModel

Direct Known Subclasses:

ArabidopsisSeed, Part, Plasmid, Strain

@Entity
 @Indexed(index="Entry")
 @FullTextFilterDef(name="security",impl=EntrySecurityFilterFactory.class,cache=INSTANCE_ONLY) @FullTextFilterDef(name="boolean",impl=EntryHasFilterFactory.class,cache=INSTANCE_ONLY)
 @AnalyzerDef(name="customanalyzer",tokenizer=@TokenizerDef(factory=org.apache.lucene.analysis.standard.StandardTokenizerFactory.class),filters={@TokenFilterDef(factory=org.apache.lucene.analysis.core.LowerCaseFilterFactory.class),@TokenFilterDef(factory=org.apache.lucene.analysis.pattern.PatternReplaceFilterFactory.class,params={,})})
public class Entry
extends Object
implements DataModel

Entry class is the most important class in gd-ice. Other record types extend this class.

Entry class represent the unique handle for each record in the system. It provides the common fields, such as the recordId (uuid), timestamps, owner and creator information, etc.

Description of Entry fields:

• id: database id of an entry.
• recordId: 36 character globally unique identifier. Implemented as UUIDv4.
• versionId: 36 character globally unique identifier.
• recordType: The type of record. Currently there are plasmids, strains, arabidopsis seeds, and parts. Parts represent linear DNA in a packaging format, such as Biobricks, or raw DNA for ligationless assembly.
• owner: Owner is the person that has complete read and write access to a part. This field is the user friendly string, such as their full name, and is not used by the system for identification and association. See ownerEmail for that functionality. This field is also distinct from the creator field.
• ownerEmail: Email address of the owner. Because an entry can be exchanged between different registries, without having the corresponding account records be exchanged along with it, association of entry with a user is done through this field, instead of the database id of Account. This means that other classes (such as .entry.sample.model.Sample) also associate via the email address. Consequently, email address must be unique to a gd-ice instance.
• creator: Creator is the person that has created this entry. If the entry came from somewhere else, or was entered into this instance of gd-ice by someone other than the creator, then the owner and the creator fields would be different. This field is the user friendly string, such as their full name, and is not used by the system for identification and association.
• creatorEmail: Email address of the creator. For some very old entries, or entries that came from a third party, email address maybe empty.
• alias: Comma separated list of alias names.
• keywords: Comma separated list of keywords.
• status: Status of this entry. Currently the options are complete, in progress, or planned. This field in the future should be used to filter search results.
• shortDescription: A summary of the entry in a few words. This is what is displayed in the search result summaries, and brevity is best.
• longDescription: Longer description for the entry. Details that are not part of the summary description should be placed in this field. This field accepts markup text of different styles. see longDescriptionType
• longDescriptionType: Markup syntax used for long description. Currently plain text, mediawiki, and confluence markup syntax is supported./
• references: References for this entry.
• creationTime: Timestamp of creation of this entry.
• modificationTime: Timestamp of last modification of this entry.
• bioSafetyLevel: The biosafety level of this entry. In the future, this field will propagate to other entries, so that a strain entry holding a higher level bioSafetyLevel plasmid entry will inherit the higher bioSafetyLevel.
• intellectualProperty: Information about intellectual property (patent filing numbers, etc) for this entry.
• selectionMarkers: SelectionMarkers for this entry. In the future, this field will propagate to other entries based on inheritance.
• links: URL or other links that point outside of this instance of gd-ice.
• name: name for this entry.
• partNumber: human readable unique identifier for this entry.
• parameters: Parameters for this entry.

Author:

Timothy Ham, Zinovii Dmytriv, Hector Plahar

Constructor Summary

Constructors

Constructor and Description
Entry()

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj)
String	getAlias()
Set<Attachment>	getAttachments()
Integer	getBioSafetyLevel()
Date	getCreationTime()
String	getCreator()
String	getCreatorEmail()
Set<Folder>	getFolders()
String	getFundingSource()
long	getId()
String	getIntellectualProperty()
String	getKeywords()
Set<Entry>	getLinkedEntries()
Set<Link>	getLinks()
String	getLongDescription()
String	getLongDescriptionType()
Date	getModificationTime()
String	getName()
String	getOwner()
String	getOwnerEmail()
List<Parameter>	getParameters()
String	getPartNumber()
Set<Permission>	getPermissions()
String	getPrincipalInvestigator()
String	getPrincipalInvestigatorEmail()
String	getRecordId()
String	getRecordType()
String	getReferences()
Set<Sample>	getSamples()
Set<SelectionMarker>	getSelectionMarkers()
String	getSelectionMarkersAsString()
Sequence	getSequence()
String	getShortDescription()
String	getStatus()
String	getVersionId()
Integer	getVisibility()
int	hashCode()
void	setAlias(String alias)
void	setBioSafetyLevel(Integer bioSafetyLevel)
void	setCreationTime(Date creationTime)
void	setCreator(String creator)
void	setCreatorEmail(String creatorEmail)
void	setFundingSource(String fundingSource)
void	setId(long id)
void	setIntellectualProperty(String intellectualProperty)
void	setKeywords(String keywords)
void	setLinks(Set<Link> inputLinks)
void	setLongDescription(String longDescription)
void	setLongDescriptionType(String longDescriptionType)
void	setModificationTime(Date modificationTime)
void	setName(String name)
void	setOwner(String owner)
void	setOwnerEmail(String ownerEmail)
void	setParameters(List<Parameter> inputParameters)
void	setPartNumber(String partNumber)
void	setPrincipalInvestigator(String principalInvestigator)
void	setPrincipalInvestigatorEmail(String principalInvestigatorEmail)
void	setRecordId(String recordId)
void	setRecordType(String recordType)
void	setReferences(String references)
void	setSelectionMarkers(Set<SelectionMarker> inputSelectionMarkers)
void	setSequence(Sequence sequence)
void	setShortDescription(String shortDescription)
void	setStatus(String status)
void	setVersionId(String versionId)
void	setVisibility(Integer visibility)
PartData	toDataTransferObject()

Methods inherited from class java.lang.Object

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

Constructor Detail

Entry

public Entry()

Method Detail

getId

public long getId()

Specified by:

getId in interface DataModel

setId

public void setId(long id)

getRecordId

public String getRecordId()

setRecordId

public void setRecordId(String recordId)

getVersionId

public String getVersionId()

setVersionId

public void setVersionId(String versionId)

getRecordType

public String getRecordType()

setRecordType

public void setRecordType(String recordType)

getOwner

public String getOwner()

setOwner

public void setOwner(String owner)

getOwnerEmail

public String getOwnerEmail()

setOwnerEmail

public void setOwnerEmail(String ownerEmail)

getCreator

public String getCreator()

setCreator

public void setCreator(String creator)

getCreatorEmail

public String getCreatorEmail()

setCreatorEmail

public void setCreatorEmail(String creatorEmail)

getStatus

public String getStatus()

setStatus

public void setStatus(String status)

getAlias

public String getAlias()

setAlias

public void setAlias(String alias)

getSelectionMarkers

public Set<SelectionMarker> getSelectionMarkers()

getSelectionMarkersAsString

public String getSelectionMarkersAsString()

setSelectionMarkers

public void setSelectionMarkers(Set<SelectionMarker> inputSelectionMarkers)

getLinks

public Set<Link> getLinks()

setLinks

public void setLinks(Set<Link> inputLinks)

getKeywords

public String getKeywords()

setKeywords

public void setKeywords(String keywords)

getShortDescription

public String getShortDescription()

setShortDescription

public void setShortDescription(String shortDescription)

getLongDescription

public String getLongDescription()

setLongDescription

public void setLongDescription(String longDescription)

getLongDescriptionType

public String getLongDescriptionType()

setLongDescriptionType

public void setLongDescriptionType(String longDescriptionType)

getReferences

public String getReferences()

setReferences

public void setReferences(String references)

getCreationTime

public Date getCreationTime()

setCreationTime

public void setCreationTime(Date creationTime)

getModificationTime

public Date getModificationTime()

setModificationTime

public void setModificationTime(Date modificationTime)

setBioSafetyLevel

public void setBioSafetyLevel(Integer bioSafetyLevel)

getBioSafetyLevel

public Integer getBioSafetyLevel()

setIntellectualProperty

public void setIntellectualProperty(String intellectualProperty)

getVisibility

public Integer getVisibility()

setVisibility

public void setVisibility(Integer visibility)

getIntellectualProperty

public String getIntellectualProperty()

setParameters

public void setParameters(List<Parameter> inputParameters)

getParameters

public List<Parameter> getParameters()

getPermissions

public Set<Permission> getPermissions()

hashCode

public int hashCode()

Overrides:

hashCode in class Object

getFolders

public Set<Folder> getFolders()

getName

public String getName()

setName

public void setName(String name)

getPartNumber

public String getPartNumber()

setPartNumber

public void setPartNumber(String partNumber)

getLinkedEntries

public Set<Entry> getLinkedEntries()

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

getFundingSource

public String getFundingSource()

setFundingSource

public void setFundingSource(String fundingSource)

getPrincipalInvestigator

public String getPrincipalInvestigator()

setPrincipalInvestigator

public void setPrincipalInvestigator(String principalInvestigator)

getSamples

public Set<Sample> getSamples()

getAttachments

public Set<Attachment> getAttachments()

getSequence

public Sequence getSequence()

setSequence

public void setSequence(Sequence sequence)

toDataTransferObject

public PartData toDataTransferObject()

Specified by:

toDataTransferObject in interface DataModel

getPrincipalInvestigatorEmail

public String getPrincipalInvestigatorEmail()

setPrincipalInvestigatorEmail

public void setPrincipalInvestigatorEmail(String principalInvestigatorEmail)