/** Try and convert an object to a List. */
private List<?> toList(Object o) {
Class<?> c = o.getClass();
if (!c.isArray()) {
return null;
}
if (c.getComponentType().isPrimitive()) {
if (o instanceof boolean[]) {
return Arrays.asList(ArrayUtils.toObject((boolean[]) o));
} else if (o instanceof byte[]) {
return Arrays.asList(ArrayUtils.toObject((byte[]) o));
} else if (o instanceof short[]) {
return Arrays.asList(ArrayUtils.toObject((short[]) o));
} else if (o instanceof int[]) {
return Arrays.asList(ArrayUtils.toObject((int[]) o));
} else if (o instanceof long[]) {
return Arrays.asList(ArrayUtils.toObject((long[]) o));
} else if (o instanceof float[]) {
return Arrays.asList(ArrayUtils.toObject((float[]) o));
} else if (o instanceof double[]) {
return Arrays.asList(ArrayUtils.toObject((double[]) o));
} else if (o instanceof char[]) {
return Arrays.asList(ArrayUtils.toObject((char[]) o));
} else {
throw new RuntimeException("Unhandled primitive type");
}
} else {
return Arrays.asList((Object[]) o);
}
}
public void deleteFile(
String user, String password, String file, String recursive, int... status) {
getMock("WEBHDFS")
.expect()
.method("DELETE")
.pathInfo("/v1" + file)
.queryParam("user.name", user)
.queryParam("op", "DELETE")
.queryParam("recursive", recursive)
.respond()
.status(status[0]);
given()
// .log().all()
.auth()
.preemptive()
.basic(user, password)
.header("X-XSRF-Header", "jksdhfkhdsf")
.queryParam("op", "DELETE")
.queryParam("recursive", recursive)
.expect()
// .log().all()
.statusCode(isIn(ArrayUtils.toObject(status)))
.when()
.delete(getUrl("WEBHDFS") + "/v1" + file + (isUseGateway() ? "" : "?user.name=" + user));
assertComplete();
}
@Test
public void testPrimitiveArray() {
final int[] beast = {6, 6, 6};
assertEquals(
Arrays.asList(ArrayUtils.toObject(beast)),
therianContext.eval(
Convert.to(new TypeLiteral<List<Integer>>() {}, Positions.readOnly(beast))));
}
/** {@inheritDoc} */
@Override
public Integer[] getFromFile() {
if (getPropertiesFile().containsKey(getKey())) {
return ArrayUtils.toObject(getPropertiesFile().getIntArray(getKey(), getSpacer()));
} else {
return new Integer[0];
}
}
@Override
public Loader<Cursor> onCreateLoader(int arg0, Bundle arg1) {
if (getActivity() == null) {
return null;
}
String selection =
KEY_PARENTID
+ " is null AND "
+ KEY_ROWID
+ " NOT IN ("
+ Joiner.on(',').join(ArrayUtils.toObject(getArguments().getLongArray(KEY_EXCLUDED_ID)))
+ ")";
CursorLoader cursorLoader =
new CursorLoader(
getActivity(), TransactionProvider.CATEGORIES_URI, projection, selection, null, null);
return cursorLoader;
}
public String submitPig(
String user,
String password,
String group,
String file,
String arg,
String statusDir,
int... status) {
getMock("WEBHCAT")
.expect()
.method("POST")
.pathInfo("/v1/pig")
.respond()
.status(status[0])
.contentType("application/json")
.content("{\"id\":\"job_201210301335_0086\"}".getBytes());
String json =
given()
// .log().all()
.auth()
.preemptive()
.basic(user, password)
.header("X-XSRF-Header", "jksdhfkhdsf")
// BUG: The identity asserter needs to check for this too.
.formParam("user.name", user)
.formParam("group", group)
.formParam("file", file)
.formParam("arg", arg)
.formParam("statusdir", statusDir)
.expect()
// .log().all();
.statusCode(isIn(ArrayUtils.toObject(status)))
.contentType("application/json")
// .content( "boolean", equalTo( true ) )
.when()
.post(getUrl("WEBHCAT") + "/v1/pig" + (isUseGateway() ? "" : "?user.name=" + user))
.asString();
log.trace("JSON=" + json);
String job = from(json).getString("id");
log.debug("JOB=" + job);
assertComplete();
return job;
}
@Override
public DocScoreList mostSimilar(String phrase, int maxResults, TIntSet validIds)
throws IOException {
final TIntDoubleHashMap scores = getConceptVector(phrase, validIds);
Integer luceneIds[] = ArrayUtils.toObject(scores.keys());
Arrays.sort(
luceneIds,
new Comparator<Integer>() {
@Override
public int compare(Integer id1, Integer id2) {
return -1 * new Double(scores.get(id1)).compareTo(scores.get(id2));
}
});
DocScoreList result = new DocScoreList(Math.min(luceneIds.length, maxResults));
for (int i = 0; i < result.numDocs(); i++) {
result.set(i, esaHelper.luceneIdToWpId(luceneIds[i]), scores.get(luceneIds[i]));
}
return normalize(result);
}
@Test
public void testPerReadAlleleLikelihoodMap() {
final PerReadAlleleLikelihoodMap map = new PerReadAlleleLikelihoodMap();
final Allele alleleA = Allele.create("A");
final double lik = -1.0; // ignored
final int[] MQs = {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, QualityUtils.MAPPING_QUALITY_UNAVAILABLE};
final List<Integer> MQsList = Arrays.asList(ArrayUtils.toObject(MQs));
// MQ 255 are excluded from the calculations, we test it here.
final List<Integer> MQsListOK = new ArrayList<>(MQsList);
// NOTE: if we just call remove(i), Java thinks i is an index.
// A workaround for this overloading bogosity to to call removeAll and pass a collection
// (casting i to (Object) would work too but it's more error prone)
MQsListOK.removeAll(Collections.singleton(QualityUtils.MAPPING_QUALITY_UNAVAILABLE));
final int n1A = MQs.length;
for (int i = 0; i < n1A; i++) {
final GATKRead read = ArtificialReadUtils.createArtificialRead(TextCigarCodec.decode("10M"));
read.setMappingQuality(MQs[i]);
map.add(read, alleleA, lik);
}
final Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap =
Collections.singletonMap("sample1", map);
final VariantContext vc = makeVC();
final ReferenceContext referenceContext = null;
final Map<String, Object> annotate =
new RMSMappingQuality().annotate(referenceContext, vc, perReadAlleleLikelihoodMap);
Assert.assertEquals(annotate.size(), 1, "size");
Assert.assertEquals(
annotate.keySet(), Collections.singleton(VCFConstants.RMS_MAPPING_QUALITY_KEY), "annots");
final double rms = MathUtils.rms(MQsListOK); // only those are MQ0
Assert.assertEquals(
annotate.get(VCFConstants.RMS_MAPPING_QUALITY_KEY), String.format("%.2f", rms));
}