@Test(enabled = true)
public void sendToDifiTest() throws URISyntaxException {
OperationalMode modeOfOperation = globalConfiguration.getModeOfOperation();
assertEquals(modeOfOperation, OperationalMode.TEST, "This test may only be run in TEST mode");
URL resource = MainIT.class.getClassLoader().getResource("BII04_T10_EHF-v2.0_invoice.xml");
URI uri = resource.toURI();
File testFile = new File(uri);
assertTrue(testFile.canRead(), "Can not locate " + testFile);
String[] args = {
"-f", testFile.toString(),
"-r", WellKnownParticipant.DIFI_TEST.toString(),
"-s", WellKnownParticipant.U4_TEST.toString(),
"-t", "true",
"-e", "/tmp" // current directory
};
// Executes the outbound message sender
try {
Main.main(args);
} catch (Exception e) {
fail("Failed " + e.getMessage(), e);
}
}
@Test(enabled = false)
public void sendToEspapTest() throws URISyntaxException {
OperationalMode modeOfOperation = globalConfiguration.getModeOfOperation();
assertEquals(modeOfOperation, OperationalMode.TEST, "This test may only be run in TEST mode");
URL resource = MainIT.class.getClassLoader().getResource("BII04_T10_EHF-v2.0_invoice.xml");
URI uri = resource.toURI();
File testFile = new File(uri);
assertTrue(testFile.canRead(), "Can not locate " + testFile);
String[] args = {
"-f", testFile.toString(),
"-r", "9946:ESPAP",
"-s", WellKnownParticipant.DIFI_TEST.toString(),
"-t", "true",
"-u", "https://ap1.espap.pt/oxalis/as2",
"-m", "AS2",
"-i", "APP_1000000222"
};
// Executes the outbound message sender
try {
Main.main(args);
} catch (Exception e) {
fail("Failed " + e.getMessage());
}
}
@Test
public void testMain() throws Exception {
String inputDir = testFilesFolder + fileSep + "trityper";
String inputExprs = testFilesFolder + fileSep + "Geuvadis_CEU_YRI_Expr.txt.gz";
String inputExprsAnnot = testFilesFolder + fileSep + "Geuvadis_CEU_YRI_Annot.txt";
String inputGte = testFilesFolder + fileSep + "Geuvadis_CEU_gte.txt";
System.out.println(inputDir);
Main.main(
"--mode",
"metaqtl",
"--in",
inputDir,
"--out",
tmpOutputFolder.getAbsolutePath(),
"--cis",
"--perm",
"10",
"--inexp",
inputExprs,
"--inexpannot",
inputExprsAnnot,
"--inexpplatform",
"Ensembl_v.71",
"--gte",
inputGte,
"--skipqqplot",
"--skipdotplot",
"--rseed",
"0");
QTLTextFile eExp =
new QTLTextFile(
testFilesFolder + fileSep + "TestOutput" + fileSep + "Cis-CEU-eQTLsFDR0.05.txt",
QTLTextFile.R);
QTLFileSorter r = new QTLFileSorter();
r.run(
tmpOutputFolder.getAbsolutePath() + fileSep + "eQTLsFDR0.05.txt",
tmpOutputFolder.getAbsolutePath() + fileSep + "eQTLsFDR0.05_S.txt");
QTLTextFile eActual =
new QTLTextFile(
tmpOutputFolder.getAbsolutePath() + fileSep + "eQTLsFDR0.05_S.txt", QTLTextFile.R);
Iterator<EQTL> eExpIterator = eExp.getEQtlIterator();
Iterator<EQTL> eActualIterator = eActual.getEQtlIterator();
while (eExpIterator.hasNext() && eActualIterator.hasNext()) {
assertTrue(eActualIterator.next().sameQTL(eExpIterator.next()), "eQTL not identical");
}
assertFalse(eExpIterator.hasNext(), "not all expected eQTL are found");
assertFalse(eActualIterator.hasNext(), "found more eQTL than expected");
}