@Transactional
private void loadFile(String filename)
throws IOException, ParsingException, FileNotFoundException, DataError {
File file = new File(filename);
EmblFile emblFile = new EmblFile(file, new FileReader(file));
loader.load(emblFile);
logger.debug("Finished loading");
}
/**
* Reload the same file as before, with the <tt>overwriteExisting</tt> flag set.
*
* @throws ParsingException
* @throws IOException
*/
public void reload() throws IOException, ParsingException {
if (this.filename == null) {
throw new IllegalStateException("Filename not set");
}
logger.info("Reloading file: " + filename);
loader.setOverwriteExisting(OverwriteExisting.YES);
loadFile(filename);
}
private void doLoad(
String organismCommonName,
String organismGenus,
String organismSpecies,
String organismStrain,
String filename)
throws IOException, ParsingException {
if (organismGenus != null) {
createOrganismIfNecessary(organismCommonName, organismGenus, organismSpecies, organismStrain);
}
loader.setReportUnusedQualifiers(true);
loader.setOrganismCommonName(organismCommonName);
loadFile(filename);
this.filename = filename;
}
private void quickAndDirty() {
alwaysSkip();
loader.setContinueOnError(true);
continueOnError = true;
}
@Override
protected void processFile(File inputFile, Reader reader) throws IOException, ParsingException {
EmblFile emblFile =
new EmblFile(inputFile, reader, continueOnError, loader.getOverwriteExisting());
loader.load(emblFile);
}
private LoadEmbl(
String organismCommonName,
String overwriteExistingString,
String topLevelFeatureType,
boolean sloppyControlledCuration,
boolean goTermErrorsAreNotFatal,
String ignoreQualifiers,
String ignoreFeatures) {
EmblLoader.OverwriteExisting overwriteExisting;
if (overwriteExistingString.equals("yes")) {
overwriteExisting = EmblLoader.OverwriteExisting.YES;
} else if (overwriteExistingString.equals("no")) {
overwriteExisting = EmblLoader.OverwriteExisting.NO;
} else if (overwriteExistingString.equals("merge")) {
overwriteExisting = EmblLoader.OverwriteExisting.MERGE;
} else {
throw new RuntimeException(
"Unrecognised value for load.overwriteExisting: " + overwriteExistingString);
}
ApplicationContext applicationContext =
new ClassPathXmlApplicationContext(new String[] {"Load.xml"});
// set this to true if you want to find out what the actual database connection is.
boolean debug = false;
if (debug == true) {
org.apache.commons.dbcp.BasicDataSource ds =
applicationContext.getBean("dataSource", org.apache.commons.dbcp.BasicDataSource.class);
logger.info("Connecting to " + ds.getUrl() + " with username " + ds.getUsername());
}
this.loader = applicationContext.getBean("emblLoader", EmblLoader.class);
loader.setOrganismCommonName(organismCommonName);
loader.setOverwriteExisting(overwriteExisting);
loader.setSloppyControlledCuration(sloppyControlledCuration);
loader.setGoTermErrorsAreNotFatal(goTermErrorsAreNotFatal);
if (topLevelFeatureType.equals("chromosome")) {
loader.setTopLevelFeatureClass(Chromosome.class);
} else if (topLevelFeatureType.equals("supercontig")) {
loader.setTopLevelFeatureClass(Supercontig.class);
} else if (topLevelFeatureType.equals("contig")) {
loader.setTopLevelFeatureClass(Contig.class);
} else if (topLevelFeatureType.equals("plasmid")) {
loader.setTopLevelFeatureClass(Plasmid.class);
} else if (topLevelFeatureType.equals("EST")) {
loader.setTopLevelFeatureClass(EST.class);
} else if (topLevelFeatureType.equals("BAC_end")) {
loader.setTopLevelFeatureClass(BACEnd.class);
} else if (topLevelFeatureType.equals("gene")) {
loader.setTopLevelFeatureClass(Gene.class);
} else {
throw new RuntimeException(
String.format("Unrecognised value for load.topLevel: '%s'", topLevelFeatureType));
}
if (ignoreQualifiers != null) {
Matcher ignoreQualifiersMatcher = ignoreQualifiersPattern.matcher(ignoreQualifiers);
int end = 0;
while (ignoreQualifiersMatcher.find()) {
end = ignoreQualifiersMatcher.end();
String feature = ignoreQualifiersMatcher.group(1);
String qualifier = ignoreQualifiersMatcher.group(2);
if (feature == null) {
loader.ignoreQualifier(qualifier);
} else {
loader.ignoreQualifier(qualifier, feature);
}
}
if (end < ignoreQualifiersMatcher.regionEnd()) {
throw new RuntimeException("Failed to parse load.ignoreQualifiers: " + ignoreQualifiers);
}
}
if (ignoreFeatures != null) {
Matcher ignoreFeaturesMatcher = ignoreFeaturesPattern.matcher(ignoreFeatures);
while (ignoreFeaturesMatcher.find()) {
loader.ignoreFeature(ignoreFeaturesMatcher.group(1));
}
}
}
