Package edu.mayo.bsi.ngsportal

Class Summary

AddNGSPortalMetadata	This class creates a command line tool that takes a file whose comma delimited lines are of the form:
AddSecondaryAnalysis	Class for app that adds secondary analysis via an HTTP call to the servlet
CompareToRLIMS	@author Gregory Dougherty
CopyUserPermissions	Class for app that copies user permissions (i.e.
CreateSecondaryProject	Class for app that creates a secondary analysis project via an HTTP call to the servlet
DateUtilTester	@author Phani
DBAddSecondaryAnalysis	Class for app that adds secondary analysis directly to the database
EmailTester	Class that needs an explanation
GetRunSamples	Get all the samples for a run from the database and print the results in the following order: Run Name Flow Cell Instrument RLIMS BatchID Start Date Primary Analysis Status Instrument Complete Date Primary Complete Date Primary QC Complete Date Primary Delivery Date Sample Name Sample RLIMS ID Sequencing RLIMS Project ID Lane App Type Read Type Num Cycles Is Control Is Vendor Index Index Sequence
GetRunSequences	Get a count of all the samples for a run from the database and print the results in the following order: Run Name Num Sequences If the run does not exist in the DB, return it with 0 sequences
GetSecondaryAnalysisDates	Get all the samples (possibly of a given application type) for all the runs from the database that had primary analysis finish within a specified time, and print the results in the following order: Run Name Application Investigator CIM BIC Primary Delivered Secondary Complete Secondary Delivered
GetTableValues	Get data from a text file and add it to the DB
LoadRLIMS	@author Gregory Dougherty
LoadRLIMSBatchIDs	@author Gregory Dougherty
LoadRLIMSRun	@author Gregory Dougherty
ParseFolders	Class for app that adds secondary analysis directly to the database
PortalTester	Class used to test features as they get added to NGSPortalService.
SetFileLocations	This class creates a command line tool that takes a file whose tab delimited lines are of the form:
UpdateRunDates	@author Gregory Dougherty