how to save CoreDocument in Stanford nlp to disk 2 - stanford-nlp

Question

Followed Professor Manning's suggestion to use the ProtobufAnnotationSerializer and did something wrong.
used serializer.writeCoreDocument on the correctly working document; Later read written file with pair = serializer.read; then used pair.second InputStream p2 = pair.second; p2 was empty resulting in a null pointer when running Pair pair3 = serializer.read(p2);
public void writeDoc(CoreDocument document, String filename ) {
AnnotationSerializer serializer = new
ProtobufAnnotationSerializer();
FileOutputStream fos = null;
try {
OutputStream ks = new FileOutputStream(filename);
ks = serializer.writeCoreDocument(document, ks);
ks.flush();
ks.close();
}catch(IOException ioex) {
logger.error("IOException "+ioex);
}
}
public void ReadSavedDoc(String filename) {
// Read
byte[]kb = null;
try {
File initialFile = new File(filename);
InputStream ks = new FileInputStream(initialFile);
ProtobufAnnotationSerializer serializer = new
ProtobufAnnotationSerializer();
InputStream kis = new
ByteArrayInputStream(ks.readAllBytes());
ks.close();
Pair<Annotation, InputStream> pair = serializer.read(kis);
InputStream p2 = pair.second;
int nump2 = p2.available();
logger.info(nump2);
byte[] ba = p2.readAllBytes();
Annotation readAnnotation = pair.first;
Pair<Annotation, InputStream> pair3 = serializer.read(p2);
kis.close();
} catch (IOException e) {
e.printStackTrace();
} catch (ClassNotFoundException e) {
e.printStackTrace();
} catch (ClassCastException e) {
e.printStackTrace();
} catch(Exception ex) {
logger.error("Exception: "+ex);
ex.printStackTrace();
}
}

Answer 1

This line is unnecessary and should be deleted:
Pair<Annotation, InputStream> pair3 = serializer.read(p2);
If you have set up readAnnotation correctly that's the end of the read/write process. p2 is empty because you have read all its contents already.
There is a clear example of how to use serialization here:
https://github.com/stanfordnlp/CoreNLP/blob/master/itest/src/edu/stanford/nlp/pipeline/ProtobufSerializationSanityITest.java
You will have to also build a CoreDocument from an Annotation.
CoreDocument readDocument = new CoreDocument(readAnnotation);