imoutsatsos

/*Helper code for selecting rows from a CSV file that satisfy certain user-defined selection criteria (the query)
 The criteria are expressed in a special Groovy Syntax that allows it to be evaluated as a Groovy Map to provide the WHERE CLAUSE components
 Author: Ioannis K. Moutsatsos
*/

/*Example Selection Criteria in Groovy Format. 
 All criteria are used in AND format
 Basic format is that of a Groovy map. You have to delimit single quotes and string map values
 The map keys are the names of the file columns that will be tested by a selection criterium
 The criteria values can be in the format of an List, Range or another Map (see examples and formatting below)

imoutsatsos

/*writes a table like delimited file from Groovy list
 works with both simple lists and lists of lists
 author IoannisK. Moutsatsos
 since Aug-2-2016
 */
/* list of lists */
//theList=[[1,"LoadData"],[2,"IdentifyPrimaryObjects"],[3,"IdentifySecondaryObjects"],[4,"MaskImage"],[5,"CorrectIlluminationCalculate"],[6,"CorrectIlluminationApply"],[7,"IdentifyPrimaryObjects"],[3,"MaskImage"],[3,"CorrectIlluminationCalculate"],[3,"CorrectIlluminationApply"],[3,"IdentifyPrimaryObjects"]]
//theList=[['ModuleIndex','ModuleName'],[1,"LoadData"],[2,"IdentifyPrimaryObjects"],[3,"IdentifySecondaryObjects"],[4,"MaskImage"],[5,"CorrectIlluminationCalculate"],[6,"CorrectIlluminationApply"],[7,"IdentifyPrimaryObjects"],[3,"MaskImage"],[3,"CorrectIlluminationCalculate"],[3,"CorrectIlluminationApply"],[3,"IdentifyPrimaryObjects"]]
/*a simple list */
theList = ["LoadData", "IdentifyPrimaryObjects", "IdentifySecondaryObjects", "MaskImage", "CorrectIlluminationCalculate", "CorrectIlluminationApply", "IdentifyPrimaryObjects", "MaskIma

imoutsatsos

/* A groovy example for inferring data types of elements in an ArrayList
* Perhaps useful for when analyzing values to be create column in database
* by IKM-July 29, 2016
*/

a=[2.345, 3.2, 4.1, 2.23]
c=[1,23,33,23,34]
d=['text','read',2,45,'how',10,234.45]
 
println "a-contains:, ${a.collect{it.getClass().simpleName}.unique()}"

imoutsatsos

/*
  Required Parameters
    vDestination: folder where files are copied
    VPropFilePath:CSV file path
    vArtifactCol: CSV file column (index-1) where file path value is located
    vArtifactPath: null for auto-discovery from full path, or a standard path where file artifacts are found
*/
//collect environment variables that may be useful for path expansion
def env = System.getenv()
def JENKINS_URL=env['JENKINS_URL']

imoutsatsos

/*
 Groovy script adds a CSV header to headless CSV files in a parent folder
 CSV files with header are saved as originalName_h.csv
*/
//The CSV header to be added
def headerPath = 'D:/mydata/data/header.csv'
def header = new File(headerPath)
assert header.exists()

def parentPath = 'D:/workspace/MySQLout'

imoutsatsos

/* 
Wells in assay plates are frequently labelled with alphanumeric identifiers (A04, E11 etc)
Script assign row/columns numbers to alphanumeric Well IDs
Note that the column is returned as a formatted String
*/

rowIds='A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,AB,AC,AD,AE,AF'.tokenize(',')
columnIds=(1..48)
plate=GroovyCollections.combinations(rowIds,columnIds.collect{String.format('%02d',it)})
assert plate.size()==1536

imoutsatsos

/*
Script example for querying the Jenkins PluginManager for plugin names
Requires the class name of the plugin, typically found in the appropriate step of the configuration file
*/
import jenkins.model.Jenkins;
import hudson.PluginWrapper;
Jenkins instance = Jenkins.getInstance();
uc= instance.getPluginManager().whichPlugin(org.biouno.unochoice.model.ScriptlerScript);
println uc.getLongName()

imoutsatsos

/* 
Creates a CSV  table from properties formatted by the following convention
prefixID.CSV_Column.Value=ObjId01,ObjId02,....,ObjId0n

Semantics of this format are that each object has a unique 'ObjId' and a 'Value' for the column header 'CSV_Column'
You would somehow first group the properties by the identifying prefix
In this example the 
  property prefixId: 'metadata.plate'
  Header CSV_Column: ['fixation','probe','cell_line']
  fixation.Value:['PFA','methanol','none']

imoutsatsos

import hudson.model.*

// get current thread / Executor
def thr = Thread.currentThread()
// get current build
def build = thr?.executable

// get job 'file-type' parameter named 'My_file
def resolver = build.buildVariableResolver
my_file=resolver.resolve("My_file")

imoutsatsos

import jenkins.*
import jenkins.model.*
import hudson.*
import hudson.model.*
import org.kohsuke.stapler.Stapler
import groovy.text.SimpleTemplateEngine

def sessionID= Stapler.getCurrentRequest().getSession().getId() 
instance = Jenkins.getInstance()
globalNodeProperties = instance.getGlobalNodeProperties()