Examples with RServeClient ubic.basecode.util.r.RServeClient used on opensource projects

Example 1 with RServeClient

use of ubic.basecode.util.r.RServeClient in project Gemma by PavlidisLab.

the class BaseAnalyzerConfigurationTest method setup.

@Before
public void setup() throws Exception {
    try {
        if (Settings.getBoolean("gemma.linearmodels.useR")) {
            rc = RConnectionFactory.getRConnection(Settings.getString("gemma.rserve.hostname", "localhost"));
            if (rc != null && rc.isConnected()) {
                connected = true;
                /*
                     * We have to disconnect right away for test to work under Windows, where only one connection is
                     * allowed at a time. The classes under test will get their own connections.
                     */
                if (rc != null && rc.isConnected() && rc instanceof RServeClient)
                    ((RServeClient) rc).disconnect();
            }
        } else {
            // not using R
            connected = true;
        }
    } catch (Exception e) {
        log.warn(e.getMessage());
    }
    /* array designs */
    arrayDesign = ArrayDesign.Factory.newInstance();
    arrayDesign.setTechnologyType(TechnologyType.ONECOLOR);
    arrayDesign.setId(1L);
    arrayDesign.setName("MG-U74Test_" + RandomStringUtils.randomAlphanumeric(12));
    arrayDesign.setPrimaryTaxon(this.getTaxon("mouse"));
    expressionExperiment = ExpressionExperiment.Factory.newInstance();
    expressionExperiment.setName("analysistest_" + RandomStringUtils.randomAlphanumeric(12));
    expressionExperiment.setId(100009L);
    expressionExperiment.setShortName(RandomStringUtils.randomAlphanumeric(12));
    /* experimental factor "area" */
    experimentalFactorA_Area = ExperimentalFactor.Factory.newInstance();
    experimentalFactorA_Area.setName("area");
    experimentalFactorA_Area.setType(FactorType.CATEGORICAL);
    experimentalFactorA_Area.setId(5001L);
    Collection<FactorValue> factorValuesA = new HashSet<>();
    factorValueA1 = FactorValue.Factory.newInstance();
    factorValueA1.setId(1001L);
    factorValueA1.setValue("cerebellum");
    Characteristic characteristicA1 = Characteristic.Factory.newInstance();
    characteristicA1.setValue(factorValueA1.getValue());
    Collection<Characteristic> characteristicsA1 = new HashSet<>();
    characteristicsA1.add(characteristicA1);
    factorValueA1.setCharacteristics(characteristicsA1);
    factorValueA1.setExperimentalFactor(experimentalFactorA_Area);
    factorValueA2 = FactorValue.Factory.newInstance();
    factorValueA2.setIsBaseline(true);
    factorValueA2.setValue("amygdala");
    factorValueA2.setId(1002L);
    Characteristic characteristicA2 = Characteristic.Factory.newInstance();
    characteristicA2.setValue(factorValueA2.getValue());
    Collection<Characteristic> characteristicsA2 = new HashSet<>();
    characteristicsA2.add(characteristicA2);
    factorValueA2.setCharacteristics(characteristicsA2);
    factorValueA2.setExperimentalFactor(experimentalFactorA_Area);
    factorValuesA.add(factorValueA1);
    factorValuesA.add(factorValueA2);
    experimentalFactorA_Area.getFactorValues().addAll(factorValuesA);
    /* experimental factor "treat" */
    experimentalFactorB = ExperimentalFactor.Factory.newInstance();
    experimentalFactorB.setName("treat");
    experimentalFactorB.setId(5002L);
    experimentalFactorB.setType(FactorType.CATEGORICAL);
    Collection<FactorValue> factorValuesB = new HashSet<>();
    FactorValue factorValueB1 = FactorValue.Factory.newInstance();
    factorValueB1.setValue("pcp");
    factorValueB1.setId(1003L);
    Characteristic characteristicB1 = Characteristic.Factory.newInstance();
    characteristicB1.setValue(factorValueB1.getValue());
    Collection<Characteristic> characteristicsB1 = new HashSet<>();
    characteristicsB1.add(characteristicB1);
    factorValueB1.setCharacteristics(characteristicsB1);
    factorValueB1.setExperimentalFactor(experimentalFactorB);
    factorValueB2 = FactorValue.Factory.newInstance();
    factorValueB2.setValue("control_group");
    factorValueB2.setId(1004L);
    Characteristic characteristicB2 = Characteristic.Factory.newInstance();
    characteristicB2.setValue(factorValueB2.getValue());
    Collection<Characteristic> characteristicsB2 = new HashSet<>();
    characteristicsB2.add(characteristicB2);
    factorValueB2.setCharacteristics(characteristicsB2);
    factorValueB2.setExperimentalFactor(experimentalFactorB);
    factorValuesB.add(factorValueB1);
    factorValuesB.add(factorValueB2);
    experimentalFactorB.getFactorValues().addAll(factorValuesB);
    /* set up the biomaterials */
    biomaterials = new ArrayList<>();
    // 2 replicates
    BioMaterial biomaterial0a = BioMaterial.Factory.newInstance();
    biomaterial0a.setName("0a");
    Collection<FactorValue> factorValuesForBioMaterial0 = new HashSet<>();
    factorValuesForBioMaterial0.add(factorValueA1);
    factorValuesForBioMaterial0.add(factorValueB1);
    biomaterial0a.getFactorValues().addAll(factorValuesForBioMaterial0);
    BioMaterial biomaterial0b = BioMaterial.Factory.newInstance();
    biomaterial0b.setName("0b");
    biomaterial0b.getFactorValues().addAll(factorValuesForBioMaterial0);
    // 2 replicates
    BioMaterial biomaterial1a = BioMaterial.Factory.newInstance();
    biomaterial1a.setName("1a");
    Collection<FactorValue> factorValuesForBioMaterial1 = new HashSet<>();
    factorValuesForBioMaterial1.add(factorValueA1);
    factorValuesForBioMaterial1.add(factorValueB2);
    biomaterial1a.getFactorValues().addAll(factorValuesForBioMaterial1);
    BioMaterial biomaterial1b = BioMaterial.Factory.newInstance();
    biomaterial1b.setName("1b");
    biomaterial1b.getFactorValues().addAll(factorValuesForBioMaterial1);
    // 2 replicates
    BioMaterial biomaterial2a = BioMaterial.Factory.newInstance();
    biomaterial2a.setName("2a");
    Collection<FactorValue> factorValuesForBioMaterial2 = new HashSet<>();
    factorValuesForBioMaterial2.add(factorValueA2);
    factorValuesForBioMaterial2.add(factorValueB1);
    biomaterial2a.getFactorValues().addAll(factorValuesForBioMaterial2);
    BioMaterial biomaterial2b = BioMaterial.Factory.newInstance();
    biomaterial2b.setName("2b");
    biomaterial2b.getFactorValues().addAll(factorValuesForBioMaterial2);
    // 2 replicates
    BioMaterial biomaterial3a = BioMaterial.Factory.newInstance();
    biomaterial3a.setName("3a");
    Collection<FactorValue> factorValuesForBioMaterial3 = new HashSet<>();
    factorValuesForBioMaterial3.add(factorValueA2);
    factorValuesForBioMaterial3.add(factorValueB2);
    biomaterial3a.getFactorValues().addAll(factorValuesForBioMaterial3);
    BioMaterial biomaterial3b = BioMaterial.Factory.newInstance();
    biomaterial3b.setName("3b");
    biomaterial3b.getFactorValues().addAll(factorValuesForBioMaterial3);
    biomaterial0a.setId(100000L);
    biomaterial0b.setId(100001L);
    biomaterial1a.setId(100002L);
    biomaterial1b.setId(100003L);
    biomaterial2a.setId(100004L);
    biomaterial2b.setId(100005L);
    biomaterial3a.setId(100006L);
    biomaterial3b.setId(100007L);
    biomaterials.add(biomaterial0a);
    biomaterials.add(biomaterial0b);
    biomaterials.add(biomaterial1a);
    biomaterials.add(biomaterial1b);
    biomaterials.add(biomaterial2a);
    biomaterials.add(biomaterial2b);
    biomaterials.add(biomaterial3a);
    biomaterials.add(biomaterial3b);
    /* set up the bioassays */
    bioAssay0a = BioAssay.Factory.newInstance();
    bioAssay0a.setName("bioassay 0a");
    bioAssay0a.setSampleUsed(biomaterial0a);
    bioAssay0a.setArrayDesignUsed(arrayDesign);
    bioAssay0b = BioAssay.Factory.newInstance();
    bioAssay0b.setName("bioassay 0b");
    bioAssay0b.setSampleUsed(biomaterial0b);
    bioAssay0b.setArrayDesignUsed(arrayDesign);
    bioAssay1a = BioAssay.Factory.newInstance();
    bioAssay1a.setName("bioassay 1a");
    bioAssay1a.setSampleUsed(biomaterial1a);
    bioAssay1a.setArrayDesignUsed(arrayDesign);
    bioAssay1b = BioAssay.Factory.newInstance();
    bioAssay1b.setName("bioassay 1b");
    bioAssay1b.setSampleUsed(biomaterial1b);
    bioAssay1b.setArrayDesignUsed(arrayDesign);
    bioAssay2a = BioAssay.Factory.newInstance();
    bioAssay2a.setName("bioassay 2a");
    bioAssay2a.setSampleUsed(biomaterial2a);
    bioAssay2a.setArrayDesignUsed(arrayDesign);
    bioAssay2b = BioAssay.Factory.newInstance();
    bioAssay2b.setName("bioassay 2b");
    bioAssay2b.setSampleUsed(biomaterial2b);
    bioAssay2b.setArrayDesignUsed(arrayDesign);
    bioAssay3a = BioAssay.Factory.newInstance();
    bioAssay3a.setName("bioassay 3a");
    bioAssay3a.setSampleUsed(biomaterial3a);
    bioAssay3a.setArrayDesignUsed(arrayDesign);
    bioAssay3b = BioAssay.Factory.newInstance();
    bioAssay3b.setName("bioassay 3b");
    bioAssay3b.setSampleUsed(biomaterial3b);
    bioAssay3b.setArrayDesignUsed(arrayDesign);
    bioAssays = new ArrayList<>();
    bioAssays.add(bioAssay0a);
    bioAssays.add(bioAssay0b);
    bioAssays.add(bioAssay1a);
    bioAssays.add(bioAssay1b);
    bioAssays.add(bioAssay2a);
    bioAssays.add(bioAssay2b);
    bioAssays.add(bioAssay3a);
    bioAssays.add(bioAssay3b);
    biomaterial0a.getBioAssaysUsedIn().add(bioAssay0a);
    biomaterial0b.getBioAssaysUsedIn().add(bioAssay0b);
    biomaterial1a.getBioAssaysUsedIn().add(bioAssay1a);
    biomaterial1b.getBioAssaysUsedIn().add(bioAssay1b);
    biomaterial2a.getBioAssaysUsedIn().add(bioAssay2a);
    biomaterial2b.getBioAssaysUsedIn().add(bioAssay2b);
    biomaterial3a.getBioAssaysUsedIn().add(bioAssay3a);
    biomaterial3b.getBioAssaysUsedIn().add(bioAssay3b);
    expressionExperiment.setBioAssays(bioAssays);
    experimentalFactors = new ArrayList<>();
    experimentalFactors.add(experimentalFactorA_Area);
    experimentalFactors.add(experimentalFactorB);
    experimentalDesign = ExperimentalDesign.Factory.newInstance();
    experimentalDesign.setName("experimental design");
    experimentalDesign.setExperimentalFactors(experimentalFactors);
    expressionExperiment.setExperimentalDesign(experimentalDesign);
    experimentalFactorA_Area.setExperimentalDesign(experimentalDesign);
    experimentalFactorB.setExperimentalDesign(experimentalDesign);
    quantitationType = QuantitationType.Factory.newInstance();
    quantitationType.setName("quantitation type");
    quantitationType.setRepresentation(PrimitiveType.DOUBLE);
    quantitationType.setType(StandardQuantitationType.AMOUNT);
    quantitationType.setIsPreferred(true);
    quantitationType.setIsMaskedPreferred(false);
    quantitationType.setIsBackground(false);
    quantitationType.setScale(ScaleType.LOG2);
    quantitationType.setIsNormalized(false);
    quantitationType.setIsBackgroundSubtracted(false);
    quantitationType.setIsRatio(false);
    expressionExperiment.getQuantitationTypes().add(quantitationType);
    bioAssayDimension = BioAssayDimension.Factory.newInstance();
    bioAssayDimension.setName("test bioassay dimension");
    bioAssayDimension.setBioAssays(bioAssays);
    this.configureVectors(biomaterials, null);
}