Method Detail

• fileLinkReport

  List<ValidationReportServiceImpl.ReportEntry> fileLinkReport()

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

  Returns:

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

  See Also:

  fileLinkReport(List)

• fileLinkReport

  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.

  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.

• fileReverseHierarchyDisplay

  String fileReverseHierarchyDisplay(Integer fileSwa)

  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?

  Parameters:

  fileSwa - SeqWare accession indicating a file.

  Returns:

  A plain text representation of a tree.