edu.mayo.bsi.ngsportal
Class GetRunSamples

java.lang.Object
  edu.mayo.bsi.ngsportal.GetRunSamples

All Implemented Interfaces:

Usage

public class GetRunSamples
extends Object
implements Usage

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

@author Gregory Dougherty

Constructor Summary

GetRunSamples()

Method Summary

static void	close() Close the connection to the servlet / db
static List<SampleData>	getRunSamples(String[] runNames, String analysisType, String pi, String[] sampleNames, String[] sampleRLIMSIds, String[] sampleFamilyIds, String[] sampleParentIds, String[] rlimsProjectIDs, int minNumReads, Date startDate, Date endDate) Get all the samples from the specified runs and print the information out in this 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
static void	main(String[] args) Parse the arguments in order to 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
String	name() Return the name of the application
static void	printResults(List<SampleData> results, boolean showPI, boolean showPIAsPath, boolean showReads) Print out the results
String	usage() Writes Usage information to a String

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GetRunSamples

public GetRunSamples()

Method Detail

main

public static final void main(String[] args)

Parse the arguments in order to 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

Parameters:

args - Arguments to parse. Specified by usage()

getRunSamples

public static List<SampleData> getRunSamples(String[] runNames,
                                             String analysisType,
                                             String pi,
                                             String[] sampleNames,
                                             String[] sampleRLIMSIds,
                                             String[] sampleFamilyIds,
                                             String[] sampleParentIds,
                                             String[] rlimsProjectIDs,
                                             int minNumReads,
                                             Date startDate,
                                             Date endDate)

Get all the samples from the specified runs and print the information out in this 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

Parameters:

runNames - Names of the run(s) that we wants the samples of, null if not restricting on that

analysisType - Name of the application type to restrict on, null if none

pi - Lan ID of PI to get samples for, null if not restricting on that

sampleNames - Names of the sample(s) that we're interested in, null if not restricting on that

sampleRLIMSIds - RLIMS IDs of the sample(s) that we're interested in, null if not restricting on that

sampleFamilyIds - RLIMS Family ID of the sample(s) that we're interested in, null if not restricting on that

sampleParentIds - Root RLIMS IDs of the sample(s) that we're interested in, null if not restricting on that

rlimsProjectIDs - RLIMS Project ID(s) of the sample(s) that we're interested in, null if not restricting on that

minNumReads - Minimum number of reads for a sample restrict on, 0 if not restricting on that

startDate - Start date, inclusive, for results, null if not restricting on that

endDate - End date, inclusive, for results, null if not restricting on that

Returns:

List of SampleData, might be empty or null

printResults

public static void printResults(List<SampleData> results,
                                boolean showPI,
                                boolean showPIAsPath,
                                boolean showReads)

Print out the results

Parameters:

results - Results to print out

showPI - If true, and showPIAsPath is false, include the PI name as lastName, firstName

showPIAsPath - If true, print out the PI as path, if there is one: lastName_firstName_lanID

showReads - If true, include the number of reads, 0 if not known

close

public static void close()

Close the connection to the servlet / db

usage

public String usage()

Writes Usage information to a String

Specified by:

usage in interface Usage

Returns:

How to use this app

See Also:

Usage.usage()

name

public String name()

Return the name of the application

Specified by:

name in interface Usage

Returns:

Name of the application

See Also:

Usage.name()