Class GeoRecord

java.lang.Object
ubic.gemma.core.loader.expression.geo.model.GeoData
ubic.gemma.core.loader.expression.geo.model.GeoRecord
All Implemented Interfaces:
Serializable
public class GeoRecord extends GeoData
Used to contain GEO summary information from the 'Browse' views.

This model is not intended for parsing GEO metadata in general, but rather get high-level metadata for browsing, use GeoPlatform, GeoSeries and GeoSample for more advanced parsing scenarios.

Author:
pavlidis
See Also:

  • Constructor Details

    • GeoRecord

      public GeoRecord()

  • Method Details

    • isDetailsIncomplete

      public boolean isDetailsIncomplete()
      True when the detailed MINiML fetch for this record failed and was tolerated (GeoRetrieveConfig.isIgnoreErrors()), so the record is returned with whatever the eutils summary gave and without sample details.

      Exists so a caller can say WHICH records it is reporting on incomplete information. GEO serves invalid MINiML for withdrawn / restricted / transiently-broken series, and the condition is usually temporary — a later pass over the same accession often succeeds.

    • getSummary

      public String getSummary()

    • getOverallDesign

      public String getOverallDesign()

    • getContactName

      public String getContactName()

    • getCorrespondingExperiments

      public Collection<Long> getCorrespondingExperiments()

    • getOrganisms

      @Nullable public Collection<String> getOrganisms()

    • getPlatform

      public String getPlatform()

    • getReleaseDate

      public Date getReleaseDate()

    • getSeriesType

      public String getSeriesType()

    • isSubSeries

      public boolean isSubSeries()

    • getSubSeriesOf

      public String getSubSeriesOf()

    • isSuperSeries

      public boolean isSuperSeries()

    • getPubMedIds

      @Nullable public List<String> getPubMedIds()

    • getMeshHeadings

      @Nullable public Collection<String> getMeshHeadings()
      MeSh headings, collected from PubMed.

    • getNumSamples

      public int getNumSamples()

    • getLibraryStrategy

      public String getLibraryStrategy()

    • getLibrarySource

      public String getLibrarySource()

    • getSampleGEOAccessions

      @Nullable public Collection<String> getSampleGEOAccessions()

    • getSampleDescriptions

      public String getSampleDescriptions()

    • getSampleDetails

      public String getSampleDetails()

    • getSampleMolecules

      public String getSampleMolecules()

    • getSampleExtractProtocols

      public String getSampleExtractProtocols()

    • getSampleLabels

      public String getSampleLabels()

    • getSampleLabelProtocols

      public String getSampleLabelProtocols()

    • getSampleDataProcessing

      public String getSampleDataProcessing()

    • isUsable

      public boolean isUsable()
      Curator judgement about whether this is loadable. False indicates a problem.

    • getPreviousClicks

      public int getPreviousClicks()
      How many times a curator has already looked at the details. this helps us track data sets we've already examined for usefulness.

    • setDetailsIncomplete

      public void setDetailsIncomplete(boolean detailsIncomplete)
      True when the detailed MINiML fetch for this record failed and was tolerated (GeoRetrieveConfig.isIgnoreErrors()), so the record is returned with whatever the eutils summary gave and without sample details.

      Exists so a caller can say WHICH records it is reporting on incomplete information. GEO serves invalid MINiML for withdrawn / restricted / transiently-broken series, and the condition is usually temporary — a later pass over the same accession often succeeds.

    • setSummary

      public void setSummary(String summary)

    • setOverallDesign

      public void setOverallDesign(String overallDesign)

    • setContactName

      public void setContactName(String contactName)

    • setCorrespondingExperiments

      public void setCorrespondingExperiments(Collection<Long> correspondingExperiments)

    • setOrganisms

      public void setOrganisms(@Nullable Collection<String> organisms)

    • setPlatform

      public void setPlatform(String platform)

    • setReleaseDate

      public void setReleaseDate(Date releaseDate)

    • setSeriesType

      public void setSeriesType(String seriesType)

    • setSubSeries

      public void setSubSeries(boolean subSeries)

    • setSubSeriesOf

      public void setSubSeriesOf(String subSeriesOf)

    • setSuperSeries

      public void setSuperSeries(boolean superSeries)

    • setPubMedIds

      public void setPubMedIds(@Nullable List<String> pubMedIds)

    • setMeshHeadings

      public void setMeshHeadings(@Nullable Collection<String> meshHeadings)
      MeSh headings, collected from PubMed.

    • setNumSamples

      public void setNumSamples(int numSamples)

    • setLibraryStrategy

      public void setLibraryStrategy(String libraryStrategy)

    • setLibrarySource

      public void setLibrarySource(String librarySource)

    • setSampleGEOAccessions

      public void setSampleGEOAccessions(@Nullable Collection<String> sampleGEOAccessions)

    • setSampleDescriptions

      public void setSampleDescriptions(String sampleDescriptions)

    • setSampleDetails

      public void setSampleDetails(String sampleDetails)

    • setSampleMolecules

      public void setSampleMolecules(String sampleMolecules)

    • setSampleExtractProtocols

      public void setSampleExtractProtocols(String sampleExtractProtocols)

    • setSampleLabels

      public void setSampleLabels(String sampleLabels)

    • setSampleLabelProtocols

      public void setSampleLabelProtocols(String sampleLabelProtocols)

    • setSampleDataProcessing

      public void setSampleDataProcessing(String sampleDataProcessing)

    • setUsable

      public void setUsable(boolean usable)
      Curator judgement about whether this is loadable. False indicates a problem.

    • setPreviousClicks

      public void setPreviousClicks(int previousClicks)
      How many times a curator has already looked at the details. this helps us track data sets we've already examined for usefulness.