Package org.labkey.remoteapi.test

Class MS2SearchClient

java.lang.Object

org.labkey.remoteapi.test.MS2SearchClient

public class MS2SearchClient
extends Object

Demo code that accepts one or more CSV files on the command line. It creates assay runs to hold the metadata from the CSV, and then initiates MS2 searches on the files. If the files are not yet available, the jobs will block until the server is notified that files are available (see PipelineFileAvailableClient). Expects to receive the path to one or more CSV files on the command line. Each CSV is required to have the following columns: FileName: the name of the mzXML or RAW file to be searched Path: the path to the file Sample: the name of the sample. Used to determine if files are fractions or independent samples. LabKeyFolder: the target folder in LabKey Server ProtocolToRun: the name of the existing search protocol to be used when searching the files If other columns are present in the CSV, they will be associated with the assay runs as run properties if the assay design includes run properties with the same names. By default looks for a config.properties in the working directory, but the location can be specified with a -config=<PATH TO CONFIG FILE> argument. Expects the following config properties: baseServerURL: base URL of the LabKey Server, such as "http://www.labkey.org" username: credentials for logging in password: credentials for logging in pipelineRoot: the path to the pipeline root for the target folder. Used to pass a relative path to the server. assayId: the rowId of the GPAT assay design to be used for storing metadata searchEngine: the name of the MS2 search engine to use. Supported values are XTandem, Sequest, and Mascot. debug: (Optional) If true, print verbose HTTP connection debugging information

Constructor Summary

Constructors

Constructor	Description
MS2SearchClient()

Method Summary

Modifier and Type	Method	Description
static void	main(String... args)

Methods inherited from class java.lang.Object

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

Constructor Details

MS2SearchClient

public MS2SearchClient()

Method Details

main

public static void main(String... args)
                 throws Exception

Throws:

Exception