Enum Class PublicationAssociationSource

java.lang.Object

java.lang.Enum<PublicationAssociationSource>

ubic.gemma.model.common.description.PublicationAssociationSource

All Implemented Interfaces:

Serializable, Comparable<PublicationAssociationSource>, Constable

public enum PublicationAssociationSource
extends Enum<PublicationAssociationSource>

Who asserted a PublicationAssociation — the authority behind the claim, as distinct from the evidence they gave for it.

The rank is the point. Precedence between competing claims about the same (experiment, publication) pair is decided by getRank(), not by write order: a source may only displace an assertion whose rank is less than or equal to its own. That is what lets an automated re-fetch coexist with a human ruling instead of silently reverting it — the property a denylist cannot offer, because a denylist is only honoured by the code paths that remember to read it, while a rank comparison is made at the one point every writer passes through (PublicationAssociationService.assertAssociation).

Concretely: GEO's !Series_pubmed_id for GSE227854 names the wrong one of the submitter's two NAR 2024 papers. A curator rejects it at rank 40; the nightly GEO refresh re-proposes it at rank 30 and is refused. No exclusion file involved.

Nested Class Summary

Nested classes/interfaces inherited from class Enum

Enum.EnumDesc<E>

Enum Constant Summary

Enum Constants

Enum Constant	Description
AGENT	A machine assertion from a curation agent (pub_finder and friends).
CURATOR	A human ruling.
EXTERNAL_IMPORT	The upstream record's own link from a non-GEO loader (CELLxGENE collection DOI, ArrayExpress, the simple-metadata loader).
GEO_SUBMITTER_LINK	GEO's !Series_pubmed_id, as written by the submitter and carried through GeoConverterImpl.convertPubMedIds.
LEGACY	Provenance unknown — the row predates this table and was backfilled from the bare INVESTIGATION.PRIMARY_PUBLICATION_FK / RELEVANT_PUBLICATIONS link, which records no authority at all.

Method Summary

Modifier and Type	Method	Description
static PublicationAssociationSource	fromDbValue(String v)	Parse the lowercase external form back into the enum.
String	getDbValue()
int	getRank()
boolean	outranks(PublicationAssociationSource held)
static PublicationAssociationSource	valueOf(String name)	Returns the enum constant of this class with the specified name.
static PublicationAssociationSource[]	values()	Returns an array containing the constants of this enum class, in the order they are declared.

Methods inherited from class Enum

clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details

CURATOR

public static final PublicationAssociationSource CURATOR

A human ruling. Outranks everything, including the upstream record — a curator who has read both candidate papers is a better authority on which one produced the data than the submitter's own cross-link.

GEO_SUBMITTER_LINK

public static final PublicationAssociationSource GEO_SUBMITTER_LINK

GEO's !Series_pubmed_id, as written by the submitter and carried through GeoConverterImpl.convertPubMedIds. Usually right, occasionally the submitter pasted the wrong one of their own papers.

EXTERNAL_IMPORT

public static final PublicationAssociationSource EXTERNAL_IMPORT

The upstream record's own link from a non-GEO loader (CELLxGENE collection DOI, ArrayExpress, the simple-metadata loader). Same standing as GEO_SUBMITTER_LINK: it is what the source said, not what we concluded.

AGENT

public static final PublicationAssociationSource AGENT

A machine assertion from a curation agent (pub_finder and friends). Outranked by both the upstream record and a curator, so a finder can propose freely without being able to overwrite either.

LEGACY

public static final PublicationAssociationSource LEGACY

Provenance unknown — the row predates this table and was backfilled from the bare INVESTIGATION.PRIMARY_PUBLICATION_FK / RELEVANT_PUBLICATIONS link, which records no authority at all. Lowest rank so anything that later states a reason wins, and so "how many links still have no recorded basis?" is one WHERE clause.

Method Details

values

public static PublicationAssociationSource[] values()

Returns an array containing the constants of this enum class, in the order they are declared.

Returns:

an array containing the constants of this enum class, in the order they are declared

valueOf

public static PublicationAssociationSource valueOf(String name)

Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum class has no constant with the specified name

NullPointerException - if the argument is null

getRank

public int getRank()

Returns:

the authority rank; higher wins. See the class javadoc — ties go to the later write, so two curators in sequence behave the way anyone would expect.

outranks

public boolean outranks(PublicationAssociationSource held)

Returns:

whether an assertion from this source may displace one currently held by held.

getDbValue

public String getDbValue()

Returns:

the lowercase external form, for use in JSON DTOs / API surfaces.

fromDbValue

public static PublicationAssociationSource fromDbValue(String v)

Parse the lowercase external form back into the enum. Accepts either case.