Constructor Detail

• ValidationReportServiceImpl

  public ValidationReportServiceImpl()

Method Detail

• fileLinkReport

  public List<ValidationReportServiceImpl.ReportEntry> fileLinkReport()

  Runs the ValidationReportService.fileLinkReport(List) including all files in the SeqWare meta db.

  Specified by:

  fileLinkReport in interface ValidationReportService

  Returns:

  A list of entries. Each entry indicates the file tested and the number of links the file has.

  See Also:

  ValidationReportService.fileLinkReport(List)

• fileReverseHierarchyDisplay

  public String fileReverseHierarchyDisplay(Integer swa)

  Produces a text representation of a reverse hierarchy tree starting at a file (indicated by the provided fileSwa). The tree included all the processing nodes that led to the creation of the file as will as all the links (sequencer_run, lane, ius, sample, experiment, study) to those processing nodes. This report is useful for answering the question: What steps led to the creation of this file?

  Specified by:

  fileReverseHierarchyDisplay in interface ValidationReportService

  Parameters:

  swa -

  Returns:

  A plain text representation of a tree.

• fileLinkReport

  public List<ValidationReportServiceImpl.ReportEntry> fileLinkReport(List<Integer> fileSwas)

  Every file must be associated with at least one processing node and this node in turn must be linked (either directly or through a parent) to one of the following: sequencer_run, lane, ius, sample, experiment or study. This report includes all files included in the given list of fileSwas (File SeqWare accesssions) and notes the number of links that exist for that file. The ideal number is 1. An orphan is indicated by the number 0. A number greater that one is not a definite error, but is worthy of investigation.

  Specified by:

  fileLinkReport in interface ValidationReportService

  Parameters:

  fileSwas - A list of file SeqWare accessions to be included in the report.

  Returns:

  A list of entries. Each entry indicates the file tested and the number of links the file has.