Class CurationCommitRequest

java.lang.Object
ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
public class CurationCommitRequest extends Object
Resolved, section-scoped inputs for one all-or-none curation commit (ExpressionExperimentService.commitCuration(ExpressionExperiment, CurationCommitRequest, boolean)). Phase 1 covers the two dataset-level sections that reuse existing ExpressionExperimentService writes cleanly — basics (name / description / short name) and publications; design / tags / sample characteristics land in later phases.

Publication identifiers are resolved to persistent BibliographicReferences by the web layer before the transaction opens, so the (possibly slow, network-bound) PubMed/CrossRef fetch does not hold the commit transaction open. Each arrives as a PublicationAssertion — the reference plus the basis given for attaching it — because the basis is what a restore has to put back along with the link.

  • Constructor Details

    • CurationCommitRequest

      public CurationCommitRequest()

  • Method Details

    • isAdvanceLinkedTickets

      public boolean isAdvanceLinkedTickets()

    • setAdvanceLinkedTickets

      public void setAdvanceLinkedTickets(boolean advanceLinkedTickets)

    • getExpectedLastUpdated

      @Nullable public Date getExpectedLastUpdated()

    • setExpectedLastUpdated

      public void setExpectedLastUpdated(@Nullable Date expectedLastUpdated)

    • isBasicsPresent

      public boolean isBasicsPresent()

    • setBasicsPresent

      public void setBasicsPresent(boolean basicsPresent)

    • getName

      @Nullable public String getName()

    • setName

      public void setName(@Nullable String name)

    • getDescription

      @Nullable public String getDescription()

    • setDescription

      public void setDescription(@Nullable String description)

    • getShortName

      @Nullable public String getShortName()

    • setShortName

      public void setShortName(@Nullable String shortName)

    • isShortNameChangeAllowed

      public boolean isShortNameChangeAllowed()

    • setShortNameChangeAllowed

      public void setShortNameChangeAllowed(boolean shortNameChangeAllowed)

    • isPublicationsPresent

      public boolean isPublicationsPresent()

    • setPublicationsPresent

      public void setPublicationsPresent(boolean publicationsPresent)

    • getPrimaryPublication

      @Nullable public PublicationAssertion getPrimaryPublication()
      The paper to attach as primary, with the basis for attaching it. The basis rides along rather than being flattened away here: a commit that names evidence has it recorded, and a snapshot replayed as a restore puts a re-attached paper back with the reason it was attached rather than as an unexplained claim.

    • setPrimaryPublication

      public void setPrimaryPublication(@Nullable PublicationAssertion primaryPublication)

    • getOtherRelevantPublications

      public List<PublicationAssertion> getOtherRelevantPublications()

    • setOtherRelevantPublications

      public void setOtherRelevantPublications(List<PublicationAssertion> otherRelevantPublications)

    • isDesignPresent

      public boolean isDesignPresent()

    • setDesignPresent

      public void setDesignPresent(boolean designPresent)

    • getProposedDesign

      @Nullable public ExperimentalDesignValueObject getProposedDesign()

    • setProposedDesign

      public void setProposedDesign(@Nullable ExperimentalDesignValueObject proposedDesign)

    • getDesignPlan

      @Nullable public DesignCommitPlan getDesignPlan()

    • setDesignPlan

      public void setDesignPlan(@Nullable DesignCommitPlan designPlan)

    • getSplitOnFactorId

      @Nullable public Long getSplitOnFactorId()

    • setSplitOnFactorId

      public void setSplitOnFactorId(@Nullable Long splitOnFactorId)

    • getSplitRationale

      @Nullable public String getSplitRationale()

    • setSplitRationale

      public void setSplitRationale(@Nullable String splitRationale)

    • isTagsPresent

      public boolean isTagsPresent()

    • setTagsPresent

      public void setTagsPresent(boolean tagsPresent)

    • getTagsToAdd

      public List<CurationCommitRequest.TagAdd> getTagsToAdd()

    • setTagsToAdd

      public void setTagsToAdd(List<CurationCommitRequest.TagAdd> tagsToAdd)

    • getReason

      @Nullable public String getReason()

    • getReasonCode

      @Nullable public String getReasonCode()

    • setReasonCode

      public void setReasonCode(@Nullable String reasonCode)

    • setReason

      public void setReason(@Nullable String reason)

    • getTagsToDelete

      public List<Long> getTagsToDelete()

    • setTagsToDelete

      public void setTagsToDelete(List<Long> tagsToDelete)

    • getTagsUnchanged

      public int getTagsUnchanged()

    • setTagsUnchanged

      public void setTagsUnchanged(int tagsUnchanged)

    • isSampleCharsPresent

      public boolean isSampleCharsPresent()

    • setSampleCharsPresent

      public void setSampleCharsPresent(boolean sampleCharsPresent)

    • getSampleCharsToAdd

      public List<CurationCommitRequest.SampleCharacteristicAdd> getSampleCharsToAdd()

    • setSampleCharsToAdd

      public void setSampleCharsToAdd(List<CurationCommitRequest.SampleCharacteristicAdd> sampleCharsToAdd)

    • getSampleCharsToDelete

      public List<Long> getSampleCharsToDelete()

    • setSampleCharsToDelete

      public void setSampleCharsToDelete(List<Long> sampleCharsToDelete)

    • getSampleCharsUnchanged

      public int getSampleCharsUnchanged()

    • setSampleCharsUnchanged

      public void setSampleCharsUnchanged(int sampleCharsUnchanged)

    • isCurationDetailsPresent

      public boolean isCurationDetailsPresent()

    • setCurationDetailsPresent

      public void setCurationDetailsPresent(boolean curationDetailsPresent)

    • getCurationDetailsNote

      @Nullable public String getCurationDetailsNote()

    • setCurationDetailsNote

      public void setCurationDetailsNote(@Nullable String curationDetailsNote)

    • getRunId

      @Nullable public String getRunId()
      The producing side's run identifier, if this commit is being applied by an agent run.

      Null for a curator commit. When non-null the commit mints a COMMIT AnnotationSet in its own transaction, so the row exists only if the commit itself succeeded.

    • setRunId

      public void setRunId(@Nullable String runId)

    • getRunProvenance

      @Nullable public AnnotationSetService.RunProvenance getRunProvenance()
      Which build produced the run named by getRunId(). Null when no run was named.

    • setRunProvenance

      public void setRunProvenance(@Nullable AnnotationSetService.RunProvenance runProvenance)

    • getRunParentProposal

      @Nullable public AnnotationSet getRunParentProposal()
      The PROPOSAL annotation set this commit applies, if it applies one. Null for an unsolicited commit.

    • setRunParentProposal

      public void setRunParentProposal(@Nullable AnnotationSet runParentProposal)

    • getSnapshotPayloadJson

      @Nullable public String getSnapshotPayloadJson()
      The dataset's current curation, serialized as the CurationDocument the commit itself accepts, to be stored as a SNAPSHOT AnnotationSet if this commit changes anything.

      Read before the commit applies, so it records what the commit displaced. Null on a dry run, which writes nothing and therefore displaces nothing.

    • setSnapshotPayloadJson

      public void setSnapshotPayloadJson(@Nullable String snapshotPayloadJson)

    • getSnapshotCreatedBy

      @Nullable public String getSnapshotCreatedBy()
      Who committed, recorded on the snapshot row so the displaced state names the commit that displaced it.

    • setSnapshotCreatedBy

      public void setSnapshotCreatedBy(@Nullable String snapshotCreatedBy)