Field Detail

• fields

  protected final Map<String,String> fields

• defaults

  protected final Map<String,String> defaults

• interactive

  protected boolean interactive

Constructor Detail

• BatchMetadataParser

  public BatchMetadataParser(Metadata metadata,
                     Map<String,String> fields,
                     boolean interactive)

Method Detail

• choiceOf

  protected String choiceOf(String sampleName,
                String title,
                String[] choices,
                String deflt)

  Handles prompting for a choice out of a list of choices using integers.

  Parameters:

  sampleName - the sample name used for the prompting message

  title - the name of the field that is being set

  choices - the list of choices for the value of 'title'

  deflt - the default choice to fall back on, which can be one of the list of 'choices'. This is the string value, not the integer.

  Returns:

• findOrganismId

  protected Integer findOrganismId(String organism)

• generateRunInfo

  protected RunInfo generateRunInfo(String runName,
                        String runDescription,
                        String studyTitle,
                        String studyDescription,
                        String studyCenterName,
                        String studyCenterProject,
                        String experimentName,
                        String experimentDescription,
                        String filePath,
                        int platformId,
                        int studyType,
                        boolean isPairedEnd,
                        String workflowType,
                        String assayType)

  Generates a RunInfo object with the given parameters. All fields are optional.

  Parameters:

  runName -

  studyTitle -

  experimentName -

  filePath -

  platformId -

  studyType -

  assayType -

  workflowType -

  Returns:

• generateLaneInfo

  protected LaneInfo generateLaneInfo(String laneNumber,
                          int studyTypeAccession)

  Generates lane info with the given parameters. Lane number needs to be given. Everything else can be null or less than 0.

  Parameters:

  laneNumber -

  studyTypeAccession -

  Returns:

• generateSampleInfo

  protected SampleInfo generateSampleInfo(String prettyName,
                              String projectCode,
                              String individualNumber,
                              String librarySourceTemplateType,
                              String tissueOrigin,
                              String tissueType,
                              String libraryType,
                              String librarySizeCode,
                              String barcode,
                              int organismId,
                              String targetedResequencing,
                              String tissuePreparation,
                              String sampleDescription,
                              String iusName,
                              String iusDescription)
                                   throws Exception

  Generates a sample info object given the fields, and prompts for null fields if the interactive flag is on. The individualNumber and projectCode are required. Everything else can be null or less than 0.

  Parameters:

  prettyName -

  projectCode -

  individualNumber -

  librarySourceTemplateType -

  tissueOrigin -

  tissueType -

  libraryType -

  librarySizeCode -

  barcode -

  organismId -

  targetedResequencing -

  tissuePreparation -

  iusDescription -

  iusName -

  Returns:

  Throws:

  Exception

• promptInteger

  protected int promptInteger(String description,
                  int deflt,
                  BatchMetadataParser.Field fieldName)
                       throws joptsimple.OptionException

  Throws:

  joptsimple.OptionException

• promptAccession

  protected int promptAccession(String description,
                    int deflt,
                    net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser.KeyVal[] values,
                    BatchMetadataParser.Field fieldName)
                         throws joptsimple.OptionException

  Throws:

  joptsimple.OptionException

• promptString

  protected String promptString(String description,
                    String deflt,
                    BatchMetadataParser.Field fieldName)
                         throws joptsimple.OptionException

  Throws:

  joptsimple.OptionException

• promptString

  protected String promptString(String sampleName,
                    String title,
                    String[] choices,
                    String deflt,
                    BatchMetadataParser.Field fieldName)

  Determine a value for a field 'title' of sample 'sampleName'. This method has different functionality depending on whether the Field is set (can be null), or the 'interactive' option is on.

  Parameters:

  sampleName - the sample name used for prompting

  title - the name of the field being set

  choices - the list of choices (Strings) that the user can select from in interactive mode

  deflt - the default string if everything else fails

  fieldName - the Field that is used for command-line defaults.

  Returns:

  the choice for the field, or an OptionException if other methods fail. This method can return null.

• promptPositiveInteger

  protected int promptPositiveInteger(String description,
                          int deflt,
                          BatchMetadataParser.Field fieldName,
                          int lowNum,
                          int highNum)

• printSampleInfo

  protected void printSampleInfo(SampleInfo info,
                     Appendable writer)

• printRunInfo

  protected void printRunInfo(RunInfo info,
                  Appendable writer)

• printLaneInfo

  protected void printLaneInfo(LaneInfo info,
                   Appendable writer)