// $HeadURL$
// $Id$
//
// Copyright © 2008, 2010, 2011, 2012 by the President and Fellows of NKI.
//
// Screensaver is an open-source project developed by the ICCB-L and NSRB labs
// at Harvard Medical School. This software is distributed under the terms of
// the GNU General Public License.
/**
* Uses the MakeDummyEntities in edu.harvard.med.screensaver.model, however it
* overrides the resultValues with simple, fixed data in stead of randomized.
* This fixed data is also used in the RUnit tests.
*/
/**
*/
package edu.harvard.med.screensaver.analysis.cellhts2;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import com.google.common.collect.ImmutableMap;
import org.apache.log4j.Logger;
import org.joda.time.LocalDate;
import edu.harvard.med.screensaver.model.activities.AdministrativeActivity;
import edu.harvard.med.screensaver.model.activities.AdministrativeActivityType;
import edu.harvard.med.screensaver.model.libraries.Library;
import edu.harvard.med.screensaver.model.libraries.LibraryType;
import edu.harvard.med.screensaver.model.libraries.LibraryWellType;
import edu.harvard.med.screensaver.model.libraries.PlateSize;
import edu.harvard.med.screensaver.model.libraries.ReagentVendorIdentifier;
import edu.harvard.med.screensaver.model.libraries.SilencingReagent;
import edu.harvard.med.screensaver.model.libraries.SilencingReagentType;
import edu.harvard.med.screensaver.model.libraries.Well;
import edu.harvard.med.screensaver.model.libraries.WellKey;
import edu.harvard.med.screensaver.model.screenresults.AssayWell;
import edu.harvard.med.screensaver.model.screenresults.AssayWellControlType;
import edu.harvard.med.screensaver.model.screenresults.DataColumn;
import edu.harvard.med.screensaver.model.screenresults.ScreenResult;
import edu.harvard.med.screensaver.model.screens.Screen;
import edu.harvard.med.screensaver.model.screens.ScreenType;
import edu.harvard.med.screensaver.model.users.AdministratorUser;
import edu.harvard.med.screensaver.test.MakeDummyEntities;
public class MakeDummyEntitiesCellHTS2
{
private static final ImmutableMap<String,AssayWellControlType> ASSAY_CONTROL_WELLS = ImmutableMap.of("A01", AssayWellControlType.ASSAY_POSITIVE_CONTROL,
"B01", AssayWellControlType.ASSAY_CONTROL,
"C01", AssayWellControlType.ASSAY_CONTROL_SHARED);
// static members
private static Logger log = Logger.getLogger(MakeDummyEntitiesCellHTS2.class);
public static Library makeSimpleDummyLibrary(int id,
ScreenType screenType,
int nPlates)
{
return makeSimpleDummyLibrary(id, screenType, nPlates, 2);
}
public static Library makeSimpleDummyLibrary(int id,
ScreenType screenType,
int nPlates,
int nrPlateColumns) {
return(makeSimpleDummyLibrary(id,screenType,nPlates,nrPlateColumns,false));
}
public static Library makeSimpleDummyLibrary(int id,
ScreenType screenType,
int nPlates,
int nrPlateColumns,
boolean inclNS)
{
int startPlate = 1;
int endPlate = startPlate + nPlates;
int nrPlateRows;
if (inclNS) {
nrPlateRows = 3;
}else {
nrPlateRows = 2;
}
int nWells = nPlates * nrPlateColumns * nrPlateRows;
Library library = new Library(null,
"library " + id,
"l" + id,
screenType,
LibraryType.COMMERCIAL,
startPlate,
endPlate,
PlateSize.WELLS_384);
library.createContentsVersion(null);
library.getLatestContentsVersion().release(new AdministrativeActivity((AdministratorUser) library.getLatestContentsVersion().getLoadingActivity().getPerformedBy(), new LocalDate(), AdministrativeActivityType.LIBRARY_CONTENTS_VERSION_RELEASE));
List<Well> wells = new ArrayList<Well>(nWells);
for (int i = 0; i < nWells; ++i) {
int plate = startPlate + (i / (nrPlateColumns * nrPlateRows));
int row = (i % (nrPlateColumns * nrPlateRows)) / nrPlateColumns;
int col = (i % (nrPlateColumns * nrPlateRows)) % nrPlateColumns;
WellKey wellKey = new WellKey(plate, row, col);
Well well = library.createWell(wellKey,
ASSAY_CONTROL_WELLS.containsKey(wellKey.getWellName()) ? LibraryWellType.EMPTY
: LibraryWellType.EXPERIMENTAL);
ReagentVendorIdentifier rvi = new ReagentVendorIdentifier("Vendor" + id, "" + i);
SilencingReagent reagent = well.createSilencingReagent(rvi, SilencingReagentType.SIRNA, "ACTG");
reagent.getVendorGene().withEntrezgeneSymbol("geneEntrezSym" + wellKey)
.withSpeciesName("species")
.withGenbankAccessionNumber("GB" + wellKey.hashCode()); wells.add(well);
}
return library;
}
public static ScreenResult makeSimpleDummyScreenResult()
{
return (makeSimpleDummyScreenResult(false, false, 2));
}
public static ScreenResult makeSimpleDummyScreenResult(boolean withExcl, boolean withNull,int nrPlateColumns){
return (makeSimpleDummyScreenResult( withExcl, withNull, nrPlateColumns,false));
}
public static ScreenResult makeSimpleDummyScreenResult(boolean withExcl, boolean withNull,int nrPlateColumns,boolean withoutA01ResultValue) {
return (makeSimpleDummyScreenResult( withExcl, withNull, nrPlateColumns,withoutA01ResultValue,false));
}
public static ScreenResult makeSimpleDummyScreenResult(boolean withExcl, boolean withNull, int nrPlateColumns,boolean withoutA01ResultValue, boolean inclNS){
return (makeSimpleDummyScreenResult( withExcl, withNull, nrPlateColumns,withoutA01ResultValue,inclNS,false));
}
public static ScreenResult makeSimpleDummyScreenResult(boolean withExcl,
boolean withNull,
int nrPlateColumns,
boolean withoutA01ResultValue,
boolean inclNS,
boolean multiChannel)
{
Screen screen = MakeDummyEntities.makeDummyScreen(1, ScreenType.RNAI);
Library library = makeSimpleDummyLibrary(1,
screen.getScreenType(),
2,
nrPlateColumns,
inclNS);
ScreenResult screenResult = screen.createScreenResult();
// create DataColumns
// Define two replicates
DataColumn normRep1 = screenResult.createDataColumn("rep1").forReplicate(1).forPhenotype("phenotype").makeNumeric(3);
DataColumn normRep2 = screenResult.createDataColumn("rep2").forReplicate(2).forPhenotype("phenotype").makeNumeric(3);
DataColumn rep1C2 = null;
DataColumn rep2C2 = null;
if (multiChannel) {
rep1C2 = screenResult.createDataColumn("c2_rep1").forReplicate(1).forChannel(2).forPhenotype("phenotype").makeNumeric(3);
rep2C2 = screenResult.createDataColumn("c2_rep2").forReplicate(2).forChannel(2).forPhenotype("phenotype").makeNumeric(3);
}
// create ResultValues
// [Well(00001:A01), Well(00001:A02), Well(00001:B01), Well(00001:B02),
// Well(00002:A01), Well(00002:A02), Well(00002:B01), Well(00002:B02)]
List<Well> wells = new ArrayList<Well>(library.getWells());
// In the library the wells are a Set and not a SortedSet
Collections.sort(wells);
// Use the same values as in RUnit tests much as possible
// [Well(00001:A01), Well(00001:A02), Well(00001:A03), Well(00001:B01),
// Well(00001:B02), Well(00001:B03), Well(00002:A01), Well(00002:A02),
// Well(00002:A03), Well(00002:B01), Well(00002:B02), Well(00002:B03)]
ArrayList<Double> rep1Values = new ArrayList<Double>();
rep1Values.add(new Double(1));
rep1Values.add(new Double(2));
rep1Values.add(new Double(3));
rep1Values.add(new Double(4));
if (inclNS) {
rep1Values.add(new Double(2));
rep1Values.add(null);
}
rep1Values.add(new Double(5));
rep1Values.add(new Double(6));
rep1Values.add(new Double(7));
rep1Values.add(new Double(9));
if (inclNS) {
rep1Values.add(new Double(4));
rep1Values.add(null);
}
ArrayList<Double> rep2Values = new ArrayList<Double>();
rep2Values.add(new Double(9));
rep2Values.add(new Double(10));
rep2Values.add(new Double(11));
rep2Values.add(new Double(14));
if (inclNS) {
rep2Values.add(new Double(6));
rep2Values.add(null);
}
rep2Values.add(new Double(13));
rep2Values.add(new Double(14));
rep2Values.add(new Double(15));
rep2Values.add(new Double(19));
if (inclNS) {
rep2Values.add(new Double(8));
rep2Values.add(null);
}
if (nrPlateColumns == 3) {
rep1Values.add(new Double(10));
rep1Values.add(new Double(11));
rep1Values.add(new Double(15));
rep1Values.add(new Double(13));
rep2Values.add(new Double(21));
rep2Values.add(new Double(23));
rep2Values.add(new Double(26));
rep2Values.add(new Double(29));
}
ArrayList<Double> rep1C2Values = new ArrayList<Double>();
ArrayList<Double> rep2C2Values = new ArrayList<Double>();
if (multiChannel) {
rep1C2Values.add(new Double(4));
rep1C2Values.add(new Double(6));
rep1C2Values.add(new Double(5));
rep1C2Values.add(new Double(6));
rep1C2Values.add(new Double(8));
rep1C2Values.add(new Double(7));
rep1C2Values.add(new Double(14));
rep1C2Values.add(new Double(16));
rep1C2Values.add(new Double(15));
rep1C2Values.add(new Double(16));
rep1C2Values.add(new Double(18));
rep1C2Values.add(new Double(17));
rep2C2Values.add(new Double(6));
rep2C2Values.add(new Double(8));
rep2C2Values.add(new Double(7));
rep2C2Values.add(new Double(8));
rep2C2Values.add(new Double(10));
rep2C2Values.add(new Double(9));
rep2C2Values.add(new Double(16));
rep2C2Values.add(new Double(18));
rep2C2Values.add(new Double(17));
rep2C2Values.add(new Double(18));
rep2C2Values.add(new Double(20));
rep2C2Values.add(new Double(19));
}
AssayWellControlType assayWellControlType = null;
for (int i = 0; i < wells.size(); ++i) {
Well well = wells.get(i);
String wellName = well.getWellKey().getWellName();
boolean exclude = false;
if (withExcl && i == 2) { // set exclude for plate 1 well B01. In case of multiple channels, all channels.
exclude = true;
}
// also test for null value
if (withNull) {
rep1Values.set(2, null);
rep2Values.set(2, null);
}
AssayWell assayWell = screenResult.createAssayWell(well);
if (ASSAY_CONTROL_WELLS.containsKey(assayWell.getLibraryWell().getWellName())) {
assayWell.setAssayWellControlType(ASSAY_CONTROL_WELLS.get(assayWell.getLibraryWell().getWellName()));
}
if (withoutA01ResultValue && wellName.equals("A01")) { }
else {
normRep1.createResultValue(assayWell, rep1Values.get(i), exclude);
normRep2.createResultValue(assayWell, rep2Values.get(i), exclude);
if (multiChannel) {
rep1C2.createResultValue(assayWell, rep1C2Values.get(i), exclude);
rep2C2.createResultValue(assayWell, rep2C2Values.get(i), exclude);
}
}
}
screen.setLibraryPlatesDataLoadedCount(2);
return screenResult;
}
}