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Posted to commits@uima.apache.org by sc...@apache.org on 2016/12/05 20:00:53 UTC
svn commit: r1772769 -
/uima/uimaj/branches/experiment-v3-jcas/uimaj-core/src/main/java/org/apache/uima/cas/impl/BinaryCasSerDes4.java
Author: schor
Date: Mon Dec 5 20:00:53 2016
New Revision: 1772769
URL: http://svn.apache.org/viewvc?rev=1772769&view=rev
Log:
[UIMA-4663] Make form 4 coding the same as v2, so can read v2. Add capability for deserialization of delta without prev deserialization of base (used in test case). handle delta changing fs ref to null properly.
Modified:
uima/uimaj/branches/experiment-v3-jcas/uimaj-core/src/main/java/org/apache/uima/cas/impl/BinaryCasSerDes4.java
Modified: uima/uimaj/branches/experiment-v3-jcas/uimaj-core/src/main/java/org/apache/uima/cas/impl/BinaryCasSerDes4.java
URL: http://svn.apache.org/viewvc/uima/uimaj/branches/experiment-v3-jcas/uimaj-core/src/main/java/org/apache/uima/cas/impl/BinaryCasSerDes4.java?rev=1772769&r1=1772768&r2=1772769&view=diff
==============================================================================
--- uima/uimaj/branches/experiment-v3-jcas/uimaj-core/src/main/java/org/apache/uima/cas/impl/BinaryCasSerDes4.java (original)
+++ uima/uimaj/branches/experiment-v3-jcas/uimaj-core/src/main/java/org/apache/uima/cas/impl/BinaryCasSerDes4.java Mon Dec 5 20:00:53 2016
@@ -44,7 +44,6 @@ import java.util.zip.DeflaterOutputStrea
import java.util.zip.Inflater;
import java.util.zip.InflaterInputStream;
-import org.apache.uima.UIMASaxException;
import org.apache.uima.UimaSerializable;
import org.apache.uima.cas.AbstractCas;
import org.apache.uima.cas.CASRuntimeException;
@@ -135,7 +134,7 @@ public class BinaryCasSerDes4 implements
private static final boolean TRACE_DOUBLE = false;
// private static final boolean TRACE_INT = false;
public static final int TYPECODE_COMPR = 8;
- public static final boolean CHANGE_FS_REFS_TO_SEQUENTIAL = true;
+// public static final boolean CHANGE_FS_REFS_TO_SEQUENTIAL = true; // currently unreferenced
// may add more later - to specify differing trade-offs between speed and compression
public enum Compression {None, Compress};
public static final boolean IS_DIFF_ENCODE = true;
@@ -360,17 +359,17 @@ public class BinaryCasSerDes4 implements
}
public SerializationMeasures serialize(AbstractCas cas, Object out, Marker trackingMark) throws IOException {
- return serialize(cas, out,trackingMark, CompressLevel.Default, CompressStrat.Default);
+ return serialize(cas, out, trackingMark, CompressLevel.Default, CompressStrat.Default);
}
public SerializationMeasures serialize(AbstractCas cas, Object out) throws IOException {
return serialize(cas, out, null);
}
- public void deserialize(CASImpl cas, InputStream deserIn, boolean isDelta, int version1) throws IOException {
- DataInput in = CommonSerDes.maybeWrapToDataInputStream(deserIn);
+ public void deserialize(CASImpl cas, InputStream deserIn, boolean isDelta, CommonSerDes.Header h) throws IOException {
+ DataInput in = (DataInput) deserIn;
Deserializer deserializer = new Deserializer(cas, in, isDelta);
- deserializer.deserialize(version1);
+ deserializer.deserialize(h);
}
/**
@@ -445,6 +444,7 @@ public class BinaryCasSerDes4 implements
final private DataOutputStream control_dos;
final private DataOutputStream strSeg_dos;
+ final private CommonSerDesSequential csds;
/**
* convert between FSs and "sequential" numbers
* This is for compression efficiency and also is needed for backwards compatibility with v2 serialization forms, where
@@ -454,7 +454,7 @@ public class BinaryCasSerDes4 implements
* Contrast with fs2addr and addr2fs in csds - these use the pseudo v2 addresses as the int
*/
private final Obj2IntIdentityHashMap<TOP> fs2seq = new Obj2IntIdentityHashMap<TOP>(TOP.class, TOP._singleton);
- private final Int2ObjHashMap<TOP> seq2fs = new Int2ObjHashMap<>(TOP.class);
+// private final Int2ObjHashMap<TOP> seq2fs = new Int2ObjHashMap<>(TOP.class);
/**
*
* @param cas -
@@ -519,6 +519,7 @@ public class BinaryCasSerDes4 implements
strSeg_dos = dosZipSources[strSeg_i];
this.prevFsByType = new TOP[ts.getTypeArraySize()];
+ csds = getCsds(baseCas, isDelta);
}
/**
@@ -542,7 +543,7 @@ public class BinaryCasSerDes4 implements
// sm.origAuxLongs = baseCas.getLongHeap().getSize() * 8;
// sm.totalTime = System.currentTimeMillis();
// }
- final CommonSerDesSequential csds = getCsds(baseCas, isDelta);
+
/************************
* Write standard header
@@ -576,12 +577,12 @@ public class BinaryCasSerDes4 implements
* done for entire cas (in the case of a mark)
*/
fs2seq.clear();
- seq2fs.clear();
+// seq2fs.clear();
int seq = 1; // origin 1
final List<TOP> localSortedFSs = csds.getSortedFSs();
for (TOP fs : localSortedFSs) {
- fs2seq.put(fs, seq);
- seq2fs.put(seq++, fs);
+ fs2seq.put(fs, seq++);
+// seq2fs.put(seq++, fs);
if (fs instanceof UimaSerializable) {
((UimaSerializable)fs)._save_to_cas_data();
}
@@ -1345,10 +1346,17 @@ public class BinaryCasSerDes4 implements
*/
for (FsChange fsChange : fsChanges) {
-
+
TOP fs = fsChange.fs;
TypeImpl ti = fs._getTypeImpl();
final int addr = csds.fs2addr.get(fs);
+ if (addr == 0) { // https://issues.apache.org/jira/browse/UIMA-5194
+ // need to write a dummy entry because we already outputted the number of changes
+ writeVnumber(fsIndexes_dos, 0);
+ // don't update iPrevAddr
+ // NOTE: modify corresponding deserialization code to detect this convention
+ continue;
+ }
// write out the address of the modified FS
writeVnumber(fsIndexes_dos, addr - iPrevAddr);
// delay updating iPrevAddr until end of "for" loop
@@ -1425,7 +1433,7 @@ public class BinaryCasSerDes4 implements
break;
case Slot_HeapRef: {
- int v = fs2seq(fs._getFeatureValueNc(feat));
+ int v = fs2seq(fs._getFeatureValueNc(feat)); // v2 writes it this way
writeDiff(kindi, v, vPrevModHeapRef);
vPrevModHeapRef = v;
break;
@@ -1531,10 +1539,16 @@ public class BinaryCasSerDes4 implements
private int fs2seq(TOP fs) {
return (fs == null) ? 0 : fs2seq.get(fs);
}
+
+
// private TOP seq2fs(int s) {
// return (s == 0) ? null : seq2fs.get(s);
// }
+
+ private int fs2addr(TOP fs) {
+ return (fs == null) ? 0 : csds.fs2addr.get(fs);
+ }
} // end of class definition for Serializer
@@ -1640,10 +1654,6 @@ public class BinaryCasSerDes4 implements
*/
final private TOP[] prevFsByType = new TOP[ts.getTypeArraySize()];
private TOP prevFs;
- /**
- * If true, adjust type codes in serialized forms > 37 up by 2
- */
- private boolean isBeforeV3;
/**
* convert between FSs and "sequential" numbers
@@ -1702,10 +1712,9 @@ public class BinaryCasSerDes4 implements
strSeg_dis = dataInputs[strSeg_i];
}
- private void deserialize(int version1) throws IOException {
+ private void deserialize(CommonSerDes.Header h) throws IOException {
if (TRACE_DES) System.out.println("Form4Deser starting");
- isBeforeV3 = (version1 & 0xff00) == 0;
-
+
// fs2seq.clear();
seq2fs.clear();
/************************************************
@@ -1774,12 +1783,11 @@ public class BinaryCasSerDes4 implements
if (TRACE_DES) System.out.println("Form4Deser heapStart: " + heapStart + " heapEnd: " + heapEnd);
for (int iHeap = heapStart; iHeap < heapEnd; iHeap += type.getFsSpaceReq(arraySize)) {
-
final int typeCode = readVnumber(typeCode_dis);
- final int adjTypeCode = typeCode + ((isBeforeV3 && typeCode > TypeSystemConstants.lastBuiltinV2TypeCode)
+ final int adjTypeCode = typeCode + ((this.bcsd.isBeforeV3 && typeCode > TypeSystemConstants.lastBuiltinV2TypeCode)
? TypeSystemConstants.numberOfNewBuiltInsSinceV2
: 0);
- type = ts.getTypeForCode(adjTypeCode);
+ type = ts.getTypeForCode(adjTypeCode);
prevFs = prevFsByType[adjTypeCode]; // could be null;
prevFsRefs = getPrevFsRef(type); // null or int[], only for things having fsrefs (array or not)
@@ -1863,7 +1871,7 @@ public class BinaryCasSerDes4 implements
prevFsByType[adjTypeCode] = currentFs;
}
-
+ csds.setHeapEnd(heapEnd);
if (TRACE_DES) System.out.println("Form4Deser running deferred fixups after all FSs deserialized");
for (Runnable r : fixupsNeeded) {
@@ -2089,6 +2097,7 @@ public class BinaryCasSerDes4 implements
final int nbrViews = readVnumber(control_dis);
final int nbrSofas = readVnumber(control_dis);
+ // fsIndexes is collection of FSs represented by sequentially incrementing numbers
IntVector fsIndexes = new IntVector(nbrViews + nbrSofas + 100);
fsIndexes.add(nbrViews);
fsIndexes.add(nbrSofas);
@@ -2162,6 +2171,7 @@ public class BinaryCasSerDes4 implements
int v = readVnumber(fsIndexes_dis) + prev;
prev = v;
// v = csds.fs2addr.get(seq2fs(v)); // v is the seq form of a ref (incr by 1)
+ // v is a sequentially incrementing ref to a FS
fsIndexes.add(v);
}
}
@@ -2435,8 +2445,13 @@ public class BinaryCasSerDes4 implements
for (int i = 0; i < modFSsLength; i++) {
iHeap = readVnumber(fsIndexes_dis) + iPrevHeap;
- iPrevHeap = iHeap;
-
+ // convention for a skipped entry: written as 0
+ boolean isSkippedEntry = iHeap == iPrevHeap;
+ if (isSkippedEntry) {
+ continue;
+ } else {
+ iPrevHeap = iHeap;
+ }
TOP fs = csds.addr2fs.get(iHeap);
assert(fs != null);
TypeImpl type = fs._getTypeImpl();
@@ -2586,8 +2601,8 @@ public class BinaryCasSerDes4 implements
int v = readDiff(heapRef_dis, vPrevModHeapRef);
vPrevModHeapRef = v;
- final TOP ref_fs = seq2fs(v);
- assert(ref_fs != null);
+ final TOP ref_fs = seq2fs(v); // v2 stores these this way
+// assert(ref_fs != null); // it could be a modification which set the slot to null
if (isArray) {
((FSArray)fs).set(offsetInFs - 2, ref_fs);
} else {
@@ -2633,6 +2648,10 @@ public class BinaryCasSerDes4 implements
private TOP seq2fs(int s) {
return (s == 0) ? null : seq2fs.get(s);
}
+
+ private TOP addr2fs(int s) {
+ return (s == 0) ? null : csds.addr2fs.get(s);
+ }
}
/* ******************************************************************