public void testWriteAssayProperties() throws AtlasLoaderException {
// create investigation
MAGETABInvestigation investigation = new MAGETABInvestigation();
investigation.IDF.experimentalFactorType.add("Type");
investigation.IDF.experimentalFactorName.add("Type");
Assay assay = new Assay("TEST-ASSAY");
AssayNode assayNode = new AssayNode();
FactorValueAttribute fva = new FactorValueAttribute();
fva.type = "Type";
fva.setAttributeValue("specific factor value");
assayNode.factorValues.add(fva);
final LoaderDAO dao = MockFactory.createLoaderDAO();
AssayAndHybridizationStep.writeAssayProperties(investigation, assay, assayNode, dao);
// now get properties of assay - we should have one matching our factor value
assertSame("Wrong number of properties", assay.getProperties().size(), 1);
for (AssayProperty p : assay.getProperties()) {
assertEquals("Wrong property name", p.getName(), "type");
assertEquals("Wrong property value", p.getValue(), "specific factor value");
}
}
protected void checkAssaysInCache() {
// parsing finished, look in our cache...
// expect 404 assays
assertEquals(
"Local cache doesn't contain correct number of assays", 404, cache.fetchAllAssays().size());
// assertEquals("Should have rejected 404 assay to sample links, as samples aren't
// loaded", 404,
// counter.intValue());
// get the title of the experiment
for (Assay assay : cache.fetchAllAssays()) {
String acc = assay.getAccession();
assertNotNull("Sample acc is null", acc);
}
// test properties of each assay
for (Assay assay : cache.fetchAllAssays()) {
List<AssayProperty> props = assay.getProperties();
// should have one property, organism
assertNotNull("Assay " + assay.getAccession() + " properties list is null", props);
assertEquals(
"More than one property observed for assay "
+ assay.getAccession()
+ ", should be Factor Value[Ecotype] only",
1,
props.size());
assertEquals("Property name is not 'Ecotype'", "ecotype", props.get(0).getName());
// test some property values at random
if (assay.getAccession().equals("E-GEOD-3790::hybridizationname::11 CN A")) {
assertEquals(
"Property value should be 'Cape Verde Islands'",
"Cape Verde Islands",
props.get(0).getValue());
}
if (assay.getAccession().equals("E-GEOD-3790::hybridizationname::81 CB A")) {
assertEquals(
"Property value should be 'Vancouver-0'", "Vancouver-0", props.get(0).getValue());
}
if (assay.getAccession().equals("E-GEOD-3790::hybridizationname::106 FC BA9 A")) {
assertEquals("Property value should be 'Shahdara'", "Shahdara", props.get(0).getValue());
}
}
}