public void testSenderDoesNotSendInvalidQuery() throws InterruptedException, ExecutionException {
BLASTQuery query = anInvalidPendingBLASTQuery();
sender.execute(query);
Integer numberSent = sender.get();
assertThat("Expected no query to be send", numberSent, is(0));
assertThat("The BLAST query's status should be draft", query.getStatus(), is(Status.DRAFT));
}
private BLASTQuery anInvalidPendingBLASTQuery() {
BLASTQuery aBLASTQuery = aBLASTQueryWithStatus(Status.PENDING);
aBLASTQuery.setSequence("");
switch (aBLASTQuery.getVendorID()) {
case BLASTVendor.EMBL_EBI:
aBLASTQuery.setSearchParameter("email", "user@@email.com");
break;
}
return aBLASTQuery;
}
public void testSenderSendsAValidQuery() throws InterruptedException, ExecutionException {
BLASTQuery query = aValidPendingBLASTQuery();
sender.execute(query);
Integer numberSent = sender.get();
assertThat("Expected the number of queries sent to be more than 1", numberSent, is(1));
assertThat(
"The BLAST query's identifier should be set",
query.getJobIdentifier(),
is(not(nullValue())));
}
public void testWeCannotDownloadResultsIfThereIsNoWebConnection()
throws InterruptedException, ExecutionException {
BLASTQuery query = BLASTQueryBuilder.aValidPendingBLASTQuery();
BLASTHitsLoaderTask downloader =
new BLASTHitsLoaderTask(context, getServiceFor(query.getVendorID())) {
protected boolean connectedToWeb() {
return false;
}
};
downloader.execute(query);
String nameOfFile = downloader.get();
assertNull("Name of file with BLAST hits", nameOfFile);
}
public void testWeCanDownloadResultsOfAFINISHEDEMBLQuery()
throws InterruptedException, ExecutionException {
BLASTQuery emblQuery = BLASTQueryBuilder.validPendingEMBLBLASTQuery();
save(emblQuery);
SendBLASTQuery.sendToEBIEMBL(context, emblQuery);
waitUntilFinished(emblQuery);
BLASTHitsLoaderTask downloader =
new BLASTHitsLoaderTask(context, getServiceFor(emblQuery.getVendorID()));
downloader.execute(emblQuery);
String nameOfFile = downloader.get();
assertNotNull("Name of file with BLAST hits being non-nulled: " + nameOfFile, nameOfFile);
assertFileOnDisk(String.format("%s.xml", emblQuery.getJobIdentifier()));
removeFileFromDisk(emblQuery);
}
private void waitUntilFinished(BLASTQuery query) throws InterruptedException, ExecutionException {
StatusTranslator translator = new StatusTranslator();
BLASTSearchEngine service = getServiceFor(query.getVendorID());
SearchStatus current = service.pollQuery(query.getJobIdentifier());
query.setStatus(translator.translate(current));
while (current.equals(SearchStatus.RUNNING)) {
current = service.pollQuery(query.getJobIdentifier());
query.setStatus(translator.translate(current));
Log.i(TAG, current.toString());
}
Log.i(TAG, "BLAST search finished. Status of query is " + query.getStatus());
}
private void removeFileFromDisk(BLASTQuery query) {
if (context.deleteFile(query.getJobIdentifier() + ".xml")) {
Log.i(TAG, "BLAST hits file deleted");
}
}