Interface ArrayDesignReportService

All Known Implementing Classes:
ArrayDesignReportServiceImpl
public interface ArrayDesignReportService
Author:
paul

  • Method Details

    • getReportDir

      String getReportDir()
      Absolute directory the cached platform reports are read from and written to.

      Exposed so callers can say where their output went. The path is derived from gemma.appdata.home, which differs between the CLI (running on the host) and gemma-rest (running in a container against a mounted volume) — a report written to the wrong one is invisible to the other with no error anywhere, which has already cost a debugging session.

    • generateAllArrayDesignReport

      void generateAllArrayDesignReport()
      Write the report summarizing all platforms.
      Throws:
      UncheckedIOException - if the report cannot be written; the previous report is left in place

    • generateArrayDesignReport

      @Secured("GROUP_AGENT") void generateArrayDesignReport()
      Generate reports for all array designs, as well as the "global" report.

      A platform whose report cannot be written is logged and skipped.

    • generateArrayDesignReport

      @Secured("GROUP_AGENT") void generateArrayDesignReport(ArrayDesignValueObject adVo)
      Generate the report for one platform.
      Throws:
      UncheckedIOException - if the report cannot be written; the previous report is left in place

    • generateArrayDesignReport

      @Secured("GROUP_AGENT") ArrayDesignValueObject generateArrayDesignReport(Long id)
      Generate the report for one platform, for callers that do so as a side effect of other work.

      A report that cannot be written is logged, not thrown, and the previous report is left in place. Use generateArrayDesignReport(ArrayDesignValueObject) to find out whether the write succeeded.

      Returns:
      the report just written, or null if the platform has no value object or the report could not be written

    • getSummaryObject

      ArrayDesignValueObject getSummaryObject(Long id)

    • getSummaryObject

      ArrayDesignValueObject getSummaryObject()

    • getSummaryObject

      Collection<ArrayDesignValueObject> getSummaryObject(Collection<Long> ids)

    • fillEventInformation

      void fillEventInformation(Collection<ArrayDesignValueObject> adVos)

    • fillInSubsumptionInfo

      void fillInSubsumptionInfo(Collection<ArrayDesignValueObject> valueObjects)

    • fillInValueObjects

      void fillInValueObjects(Collection<ArrayDesignValueObject> adVos)

    • getLastSequenceUpdateEvent

      String getLastSequenceUpdateEvent(Long id)

    • getLastSequenceAnalysisEvent

      String getLastSequenceAnalysisEvent(Long id)

    • getLastRepeatMaskEvent

      String getLastRepeatMaskEvent(Long id)

    • getLastGeneMappingEvent

      String getLastGeneMappingEvent(Long id)

    • getCreateDate

      String getCreateDate(Long id)