public void setUp() throws Exception {
tgtModel = Model.getInstanceByName("genomic");
handler = new FlyRegGFF3RecordHandler(tgtModel);
handler.rslv = IdResolverService.getMockIdResolver("Gene");
handler.rslv.addResolverEntry("7227", "FBgn001", Collections.singleton("dpp"));
handler.rslv.addResolverEntry("7227", "FBgn002", Collections.singleton("dl"));
converter =
new GFF3Converter(
writer, seqClsName, taxonId, dataSourceName, dataSetTitle, tgtModel, handler, null);
}
/**
* Process the csv file
*
* @param reader the Reader
* @see DataConverter#process
* @throws Exception if something goes wrong
*/
@Override
public void process(Reader reader) throws Exception {
if (rslv == null) {
rslv = IdResolverService.getFlyIdResolver();
}
Iterator<String[]> it = FormattedTextParser.parseTabDelimitedReader(reader);
while (it.hasNext()) {
String[] lineBits = it.next();
String geneCG = lineBits[0];
if (!geneCG.startsWith("CG")) {
// ignore clones for now
continue;
}
// Try to create/fetch gene, if null the IdResolver failed so do nothing for this row
Item gene = getGene(geneCG);
if (gene == null) {
continue;
}
String stage = lineBits[1];
String resultKey = geneCG + stage;
Item result = getResult(resultKey, gene.getIdentifier(), pub.getIdentifier(), stage);
Integer stageNumber = null;
try {
stageNumber = new Integer(stage);
} catch (NumberFormatException e) {
// bad line in file, just keep going
continue;
}
result.setAttribute("stageRange", STAGE_LABELS[stageNumber.intValue()] + " (BDGP in situ)");
if (lineBits.length > 2) {
String image = lineBits[2];
if (StringUtils.isNotEmpty(image)) {
setImage(result, URL + image);
}
}
if (lineBits.length > 3) {
String term = lineBits[3];
Item termItem = getTerm(term);
if (termItem != null) {
result.addToCollection("mRNAExpressionTerms", termItem);
}
if ("no staining".equals(term)) {
result.setAttribute("expressed", "false");
}
}
}
for (Item result : results.values()) {
if (!result.hasCollection("mRNAExpressionTerms")
|| result.getCollection("mRNAExpressionTerms").getRefIds().isEmpty()) {
result.setAttribute("expressed", "false");
}
}
storeAll(imgs);
storeAll(results);
}