static {
InputStream resource = Boot._init.getResource2("/page.html");
try {
_htmlTemplate =
new String(ByteStreams.toByteArray(resource)).replace("%cloud_name", H2O.NAME);
} catch (NullPointerException e) {
Log.err(e);
Log.die("page.html not found in resources.");
} catch (Exception e) {
Log.err(e);
Log.die(e.getMessage());
} finally {
Closeables.closeQuietly(resource);
}
}
private static void addFolder2(
FileSystem fs, Path p, ArrayList<String> keys, ArrayList<String> failed) {
try {
if (fs == null) return;
Futures futures = new Futures();
for (FileStatus file : fs.listStatus(p)) {
Path pfs = file.getPath();
if (file.isDir()) {
addFolder2(fs, pfs, keys, failed);
} else {
long size = file.getLen();
Key res;
if (pfs.getName().endsWith(Extensions.JSON)) {
throw H2O.unimpl();
} else if (pfs.getName().endsWith(Extensions.HEX)) { // Hex file?
throw H2O.unimpl();
} else {
Key k = null;
keys.add((k = HdfsFileVec.make(file, futures)).toString());
Log.info("PersistHdfs: DKV.put(" + k + ")");
}
}
}
} catch (Exception e) {
Log.err(e);
failed.add(p.toString());
}
}
private static void addFolder(FileSystem fs, Path p, JsonArray succeeded, JsonArray failed) {
try {
if (fs == null) return;
for (FileStatus file : fs.listStatus(p)) {
Path pfs = file.getPath();
if (file.isDir()) {
addFolder(fs, pfs, succeeded, failed);
} else {
Key k = Key.make(pfs.toString());
long size = file.getLen();
Value val = null;
if (pfs.getName().endsWith(Extensions.JSON)) {
JsonParser parser = new JsonParser();
JsonObject json = parser.parse(new InputStreamReader(fs.open(pfs))).getAsJsonObject();
JsonElement v = json.get(Constants.VERSION);
if (v == null) throw new RuntimeException("Missing version");
JsonElement type = json.get(Constants.TYPE);
if (type == null) throw new RuntimeException("Missing type");
Class c = Class.forName(type.getAsString());
OldModel model = (OldModel) c.newInstance();
model.fromJson(json);
} else if (pfs.getName().endsWith(Extensions.HEX)) { // Hex file?
FSDataInputStream s = fs.open(pfs);
int sz = (int) Math.min(1L << 20, size); // Read up to the 1st meg
byte[] mem = MemoryManager.malloc1(sz);
s.readFully(mem);
// Convert to a ValueArray (hope it fits in 1Meg!)
ValueArray ary = new ValueArray(k, 0).read(new AutoBuffer(mem));
val = new Value(k, ary, Value.HDFS);
} else if (size >= 2 * ValueArray.CHUNK_SZ) {
val =
new Value(
k,
new ValueArray(k, size),
Value.HDFS); // ValueArray byte wrapper over a large file
} else {
val = new Value(k, (int) size, Value.HDFS); // Plain Value
val.setdsk();
}
DKV.put(k, val);
Log.info("PersistHdfs: DKV.put(" + k + ")");
JsonObject o = new JsonObject();
o.addProperty(Constants.KEY, k.toString());
o.addProperty(Constants.FILE, pfs.toString());
o.addProperty(Constants.VALUE_SIZE, file.getLen());
succeeded.add(o);
}
}
} catch (Exception e) {
Log.err(e);
JsonObject o = new JsonObject();
o.addProperty(Constants.FILE, p.toString());
o.addProperty(Constants.ERROR, e.getMessage());
failed.add(o);
}
}
private void cancel(final String msg, JobState resultingState) {
if (resultingState == JobState.CANCELLED) {
Log.info("Job " + self() + "(" + description + ") was cancelled.");
} else {
Log.err("Job " + self() + "(" + description + ") failed.");
Log.err(msg);
}
exception = msg;
state = resultingState;
// replace finished job by a job handle
replaceByJobHandle();
DKV.write_barrier();
final Job job = this;
H2O.submitTask(
new H2OCountedCompleter() {
@Override
public void compute2() {
job.onCancelled();
}
});
}
public static byte [] unzipBytes(byte [] bs, Compression cmp) {
InputStream is = null;
int off = 0;
try {
switch(cmp) {
case NONE: // No compression
return bs;
case ZIP: {
ZipInputStream zis = new ZipInputStream(new ByteArrayInputStream(bs));
ZipEntry ze = zis.getNextEntry(); // Get the *FIRST* entry
// There is at least one entry in zip file and it is not a directory.
if( ze != null && !ze.isDirectory() ) {
is = zis;
break;
}
zis.close();
return bs; // Don't crash, ignore file if cannot unzip
}
case GZIP:
is = new GZIPInputStream(new ByteArrayInputStream(bs));
break;
default:
assert false:"cmp = " + cmp;
}
// If reading from a compressed stream, estimate we can read 2x uncompressed
assert( is != null ):"is is NULL, cmp = " + cmp;
bs = new byte[bs.length * 2];
// Now read from the (possibly compressed) stream
while( off < bs.length ) {
int len = is.read(bs, off, bs.length - off);
if( len < 0 )
break;
off += len;
if( off == bs.length ) { // Dataset is uncompressing alot! Need more space...
if( bs.length >= ValueArray.CHUNK_SZ )
break; // Already got enough
bs = Arrays.copyOf(bs, bs.length * 2);
}
}
} catch( IOException ioe ) { // Stop at any io error
Log.err(ioe);
} finally {
Utils.close(is);
}
return bs;
}
protected void err(Object tag, Object obj) {
Log.err(obj);
}
/**
* Simple GLM wrapper to enable launching GLM from command line.
*
* <p>Example input: java -jar target/h2o.jar -name=test -runMethod water.util.GLMRunner
* -file=smalldata/logreg/prostate.csv -y=CAPSULE -family=binomial
*
* @param args
* @throws InterruptedException
*/
public static void main(String[] args) throws InterruptedException {
try {
GLMArgs ARGS = new GLMArgs();
new Arguments(args).extract(ARGS);
System.out.println("==================<GLMRunner START>===================");
ValueArray ary = Utils.loadAndParseKey(ARGS.file);
int ycol;
try {
ycol = Integer.parseInt(ARGS.y);
} catch (NumberFormatException e) {
ycol = ary.getColumnIds(new String[] {ARGS.y})[0];
}
int ncols = ary.numCols();
if (ycol < 0 || ycol >= ary.numCols()) {
System.err.println("invalid y column: " + ycol);
H2O.exit(-1);
}
int[] xcols;
if (ARGS.xs.equalsIgnoreCase("all")) {
xcols = new int[ncols - 1];
for (int i = 0; i < ycol; ++i) xcols[i] = i;
for (int i = ycol; i < ncols - 1; ++i) xcols[i] = i + 1;
} else {
System.out.println("xs = " + ARGS.xs);
String[] names = ARGS.xs.split(",");
xcols = new int[names.length];
try {
for (int i = 0; i < names.length; ++i) xcols[i] = Integer.valueOf(names[i]);
} catch (NumberFormatException e) {
xcols = ary.getColumnIds(ARGS.xs.split(","));
}
}
for (int x : xcols)
if (x < 0) {
System.err.println("Invalid predictor specification " + ARGS.xs);
H2O.exit(-1);
}
GLMJob j =
DGLM.startGLMJob(
DGLM.getData(ary, xcols, ycol, null, true),
new ADMMSolver(ARGS.lambda, ARGS._alpha),
new GLMParams(Family.valueOf(ARGS.family)),
null,
ARGS.xval,
true);
System.out.print("[GLM] computing model...");
int progress = 0;
while (!j.isDone()) {
int p = (int) (100 * j.progress());
int dots = p - progress;
progress = p;
for (int i = 0; i < dots; ++i) System.out.print('.');
Thread.sleep(250);
}
Log.debug(Sys.GENLM, "DONE.");
GLMModel m = j.get();
String[] colnames = ary.colNames();
System.out.println("Intercept" + " = " + m._beta[ncols - 1]);
for (int i = 0; i < xcols.length; ++i) {
System.out.println(colnames[i] + " = " + m._beta[i]);
}
} catch (Throwable t) {
Log.err(t);
} finally { // we're done. shutdown the cloud
Log.debug(Sys.GENLM, "==================<GLMRunner DONE>===================");
UDPRebooted.suicide(UDPRebooted.T.shutdown, H2O.SELF);
}
}
/**
* Copy properties "of the same name" from one POJO to the other. If the fields are named
* consistently (both sides have fields named "_foo" and/or "bar") this acts like Apache Commons
* PojoUtils.copyProperties(). If one side has leading underscores and the other does not then the
* names are conformed according to the field_naming parameter.
*
* @param dest Destination POJO
* @param origin Origin POJO
* @param field_naming Are the fields named consistently, or does one side have underscores?
* @param skip_fields Array of origin or destination field names to skip
* @param only_fields Array of origin or destination field names to include; ones not in this list
* will be skipped
*/
public static void copyProperties(
Object dest,
Object origin,
FieldNaming field_naming,
String[] skip_fields,
String[] only_fields) {
if (null == dest || null == origin) return;
Field[] dest_fields = Weaver.getWovenFields(dest.getClass());
Field[] orig_fields = Weaver.getWovenFields(origin.getClass());
for (Field orig_field : orig_fields) {
String origin_name = orig_field.getName();
if (skip_fields != null & ArrayUtils.contains(skip_fields, origin_name)) continue;
if (only_fields != null & !ArrayUtils.contains(only_fields, origin_name)) continue;
String dest_name = null;
if (field_naming == FieldNaming.CONSISTENT) {
dest_name = origin_name;
} else if (field_naming == FieldNaming.DEST_HAS_UNDERSCORES) {
dest_name = "_" + origin_name;
} else if (field_naming == FieldNaming.ORIGIN_HAS_UNDERSCORES) {
dest_name = origin_name.substring(1);
}
if (skip_fields != null & ArrayUtils.contains(skip_fields, dest_name)) continue;
if (only_fields != null & !ArrayUtils.contains(only_fields, dest_name)) continue;
try {
Field dest_field = null;
for (Field fd : dest_fields) {
if (fd.getName().equals(dest_name)) {
dest_field = fd;
break;
}
}
if (dest_field != null) {
dest_field.setAccessible(true);
orig_field.setAccessible(true);
// Log.info("PojoUtils.copyProperties, origin field: " + orig_field + "; destination
// field: " + dest_field);
if (null == orig_field.get(origin)) {
//
// Assigning null to dest.
//
dest_field.set(dest, null);
} else if (dest_field.getType().isArray()
&& orig_field.getType().isArray()
&& (dest_field.getType().getComponentType()
!= orig_field.getType().getComponentType())) {
//
// Assigning an array to another array.
//
// You can't use reflection to set an int[] with an Integer[]. Argh.
// TODO: other types of arrays. . .
if (dest_field.getType().getComponentType() == double.class
&& orig_field.getType().getComponentType() == Double.class) {
//
// Assigning an Double[] to an double[]
//
double[] copy = (double[]) orig_field.get(origin);
dest_field.set(dest, copy);
} else if (dest_field.getType().getComponentType() == Double.class
&& orig_field.getType().getComponentType() == double.class) {
//
// Assigning an double[] to an Double[]
//
Double[] copy = (Double[]) orig_field.get(origin);
dest_field.set(dest, copy);
} else if (dest_field.getType().getComponentType() == int.class
&& orig_field.getType().getComponentType() == Integer.class) {
//
// Assigning an Integer[] to an int[]
//
int[] copy = (int[]) orig_field.get(origin);
dest_field.set(dest, copy);
} else if (dest_field.getType().getComponentType() == Integer.class
&& orig_field.getType().getComponentType() == int.class) {
//
// Assigning an int[] to an Integer[]
//
Integer[] copy = (Integer[]) orig_field.get(origin);
dest_field.set(dest, copy);
} else if (Schema.class.isAssignableFrom(dest_field.getType().getComponentType())
&& (Schema.getImplClass(
(Class<? extends Schema>) dest_field.getType().getComponentType()))
.isAssignableFrom(orig_field.getType().getComponentType())) {
//
// Assigning an array of impl fields to an array of schema fields, e.g. a
// DeepLearningParameters[] into a DeepLearningParametersV2[]
//
Class dest_component_class = dest_field.getType().getComponentType();
Schema[] translation =
(Schema[])
Array.newInstance(
dest_component_class, Array.getLength(orig_field.get(origin)));
int i = 0;
int version = ((Schema) dest).getSchemaVersion();
// Look up the schema for each element of the array; if not found fall back to the
// schema for the base class.
for (Iced impl : ((Iced[]) orig_field.get(origin))) {
if (null == impl) {
translation[i++] = null;
} else {
Schema s = null;
try {
s = Schema.schema(version, impl);
} catch (H2ONotFoundArgumentException e) {
s = ((Schema) dest_field.getType().getComponentType().newInstance());
}
translation[i++] = s.fillFromImpl(impl);
}
}
dest_field.set(dest, translation);
} else if (Schema.class.isAssignableFrom(orig_field.getType().getComponentType())
&& Iced.class.isAssignableFrom(dest_field.getType().getComponentType())) {
//
// Assigning an array of schema fields to an array of impl fields, e.g. a
// DeepLearningParametersV2[] into a DeepLearningParameters[]
//
// We can't check against the actual impl class I, because we can't instantiate the
// schema base classes to get the impl class from an instance:
// dest_field.getType().getComponentType().isAssignableFrom(((Schema)f.getType().getComponentType().newInstance()).getImplClass())) {
Class dest_component_class = dest_field.getType().getComponentType();
Iced[] translation =
(Iced[])
Array.newInstance(
dest_component_class, Array.getLength(orig_field.get(origin)));
int i = 0;
for (Schema s : ((Schema[]) orig_field.get(origin))) {
translation[i++] = s.createImpl();
}
dest_field.set(dest, translation);
} else {
throw H2O.fail(
"Don't know how to cast an array of: "
+ orig_field.getType().getComponentType()
+ " to an array of: "
+ dest_field.getType().getComponentType());
}
// end of array handling
} else if (dest_field.getType() == Key.class
&& Keyed.class.isAssignableFrom(orig_field.getType())) {
//
// Assigning a Keyed (e.g., a Frame or Model) to a Key.
//
dest_field.set(dest, ((Keyed) orig_field.get(origin))._key);
} else if (orig_field.getType() == Key.class
&& Keyed.class.isAssignableFrom(dest_field.getType())) {
//
// Assigning a Key (for e.g., a Frame or Model) to a Keyed (e.g., a Frame or Model).
//
Value v = DKV.get((Key) orig_field.get(origin));
dest_field.set(dest, (null == v ? null : v.get()));
} else if (KeyV3.class.isAssignableFrom(dest_field.getType())
&& Keyed.class.isAssignableFrom(orig_field.getType())) {
//
// Assigning a Keyed (e.g., a Frame or Model) to a KeyV1.
//
dest_field.set(
dest,
KeyV3.make(
((Class<? extends KeyV3>) dest_field.getType()),
((Keyed) orig_field.get(origin))._key));
} else if (KeyV3.class.isAssignableFrom(orig_field.getType())
&& Keyed.class.isAssignableFrom(dest_field.getType())) {
//
// Assigning a KeyV1 (for e.g., a Frame or Model) to a Keyed (e.g., a Frame or Model).
//
KeyV3 k = (KeyV3) orig_field.get(origin);
Value v = DKV.get(Key.make(k.name));
dest_field.set(dest, (null == v ? null : v.get()));
} else if (KeyV3.class.isAssignableFrom(dest_field.getType())
&& Key.class.isAssignableFrom(orig_field.getType())) {
//
// Assigning a Key to a KeyV1.
//
dest_field.set(
dest,
KeyV3.make(
((Class<? extends KeyV3>) dest_field.getType()), (Key) orig_field.get(origin)));
} else if (KeyV3.class.isAssignableFrom(orig_field.getType())
&& Key.class.isAssignableFrom(dest_field.getType())) {
//
// Assigning a KeyV1 to a Key.
//
KeyV3 k = (KeyV3) orig_field.get(origin);
dest_field.set(dest, (null == k.name ? null : Key.make(k.name)));
} else if (dest_field.getType() == Pattern.class
&& String.class.isAssignableFrom(orig_field.getType())) {
//
// Assigning a String to a Pattern.
//
dest_field.set(dest, Pattern.compile((String) orig_field.get(origin)));
} else if (orig_field.getType() == Pattern.class
&& String.class.isAssignableFrom(dest_field.getType())) {
//
// We are assigning a Pattern to a String.
//
dest_field.set(dest, orig_field.get(origin).toString());
} else if (dest_field.getType() == FrameV3.ColSpecifierV3.class
&& String.class.isAssignableFrom(orig_field.getType())) {
//
// Assigning a String to a ColSpecifier. Note that we currently support only the
// colname, not a frame name too.
//
dest_field.set(dest, new FrameV3.ColSpecifierV3((String) orig_field.get(origin)));
} else if (orig_field.getType() == FrameV3.ColSpecifierV3.class
&& String.class.isAssignableFrom(dest_field.getType())) {
//
// We are assigning a ColSpecifierV2 to a String. The column_name gets copied.
//
dest_field.set(dest, ((FrameV3.ColSpecifierV3) orig_field.get(origin)).column_name);
} else if (Enum.class.isAssignableFrom(dest_field.getType())
&& String.class.isAssignableFrom(orig_field.getType())) {
//
// Assigning a String into an enum field.
//
Class<Enum> dest_class = (Class<Enum>) dest_field.getType();
dest_field.set(dest, Enum.valueOf(dest_class, (String) orig_field.get(origin)));
} else if (Enum.class.isAssignableFrom(orig_field.getType())
&& String.class.isAssignableFrom(dest_field.getType())) {
//
// Assigning an enum field into a String.
//
Object o = orig_field.get(origin);
dest_field.set(dest, (o == null ? null : o.toString()));
} else if (Schema.class.isAssignableFrom(dest_field.getType())
&& Schema.getImplClass((Class<? extends Schema>) dest_field.getType())
.isAssignableFrom(orig_field.getType())) {
//
// Assigning an impl field into a schema field, e.g. a DeepLearningParameters into a
// DeepLearningParametersV2.
//
dest_field.set(
dest,
Schema.schema(
/* ((Schema)dest).getSchemaVersion() TODO: remove HACK!! */ 3,
(Class<? extends Iced>) orig_field.get(origin).getClass())
.fillFromImpl((Iced) orig_field.get(origin)));
} else if (Schema.class.isAssignableFrom(orig_field.getType())
&& Schema.getImplClass((Class<? extends Schema>) orig_field.getType())
.isAssignableFrom(dest_field.getType())) {
//
// Assigning a schema field into an impl field, e.g. a DeepLearningParametersV2 into a
// DeepLearningParameters.
//
Schema s = ((Schema) orig_field.get(origin));
dest_field.set(dest, s.fillImpl(s.createImpl()));
} else if ((Schema.class.isAssignableFrom(dest_field.getType())
&& Key.class.isAssignableFrom(orig_field.getType()))) {
//
// Assigning an impl field fetched via a Key into a schema field, e.g. a
// DeepLearningParameters into a DeepLearningParametersV2.
// Note that unlike the cases above we don't know the type of the impl class until we
// fetch in the body of the if.
//
Key origin_key = (Key) orig_field.get(origin);
Value v = DKV.get(origin_key);
if (null == v || null == v.get()) {
dest_field.set(dest, null);
} else {
if (((Schema) dest_field.get(dest))
.getImplClass()
.isAssignableFrom(v.get().getClass())) {
Schema s = ((Schema) dest_field.get(dest));
dest_field.set(
dest,
Schema.schema(s.getSchemaVersion(), s.getImplClass()).fillFromImpl(v.get()));
} else {
Log.err(
"Can't fill Schema of type: "
+ dest_field.getType()
+ " with value of type: "
+ v.getClass()
+ " fetched from Key: "
+ origin_key);
dest_field.set(dest, null);
}
}
} else if (Schema.class.isAssignableFrom(orig_field.getType())
&& Keyed.class.isAssignableFrom(dest_field.getType())) {
//
// Assigning a schema field into a Key field, e.g. a DeepLearningV2 into a
// (DeepLearningParameters) key.
//
Schema s = ((Schema) orig_field.get(origin));
dest_field.set(dest, ((Keyed) s.fillImpl(s.createImpl()))._key);
} else {
//
// Normal case: not doing any type conversion.
//
dest_field.set(dest, orig_field.get(origin));
}
}
} catch (IllegalAccessException e) {
Log.err(
"Illegal access exception trying to copy field: "
+ origin_name
+ " of class: "
+ origin.getClass()
+ " to field: "
+ dest_name
+ " of class: "
+ dest.getClass());
} catch (InstantiationException e) {
Log.err(
"Instantiation exception trying to copy field: "
+ origin_name
+ " of class: "
+ origin.getClass()
+ " to field: "
+ dest_name
+ " of class: "
+ dest.getClass());
}
}
}
