Kevin Ratnasekera commented on GORA-401:

[~alfonso.nishikawa] I don't have any background knowledge as you do regarding 
this issue and related issues in Apache Nutch. I had a look on the code, it 
seems like PersistentSerializer and PersistentDeserializer can be modified to 
preserve the dirty bytes. Since we are registering those 
Serializer/Deserializer for persistent data beans at Hadoop conf, all the 
serialization/de-serialization will be delegated to these classes. 

I have added simple check for dirty bytes comparison in 
TestIOUtils#testSerializeDeserialize, so that we can make whether proposed fix 
preserve the dirty bytes, after data bean is serialized and de-serializated, 
earlier checks only guarantees equality of fields between two persistent data 
Please do review and if you can provide some more directions, I can have 
detailed look into the issue.


> Serialization and deserialization of Persistent does not hold the entity 
> dirty state from Map to Reduce
> -------------------------------------------------------------------------------------------------------
>                 Key: GORA-401
>                 URL: https://issues.apache.org/jira/browse/GORA-401
>             Project: Apache Gora
>          Issue Type: Bug
>          Components: gora-core
>    Affects Versions: 0.4, 0.5
>         Environment: Tested on gora-0.4, but seems logically to hold on 
> gora-0.5. HBase backend.
>            Reporter: Alfonso Nishikawa
>            Assignee: Alfonso Nishikawa
>            Priority: Critical
>              Labels: serialization
>             Fix For: 0.8
>         Attachments: GORA-401-tests.patch, GORA-401v1.patch, 
> GORA-401v2.patch, GORA-401v3.patch, GORA-401v4.patch, GORA-401v5.patch
>   Original Estimate: 35h
>          Time Spent: 21h
>  Remaining Estimate: 14h
> After removing __g__dirty field in GORA-326, dirty field is not serialized. 
> In GORA-321 
> {{[PersistentSerializer|https://github.com/apache/gora/blob/master/gora-core/src/main/java/org/apache/gora/mapreduce/PersistentSerializer.java]}}
>  went from using 
> {{[PersistentDatumWriter|https://github.com/apache/gora/blob/apache-gora-0.3/gora-core/src/main/java/org/apache/gora/avro/PersistentDatumWriter.java](/Reader)}}
>  to Avro's {{SpecificDatumWriter}}, delegating the serialization of the dirty 
> field to Avro (but really not desirable to have that field as a main field in 
> the entities).
> The proposal is to reintroduce the {{PersistentDatumWriter/Reader}} which 
> will serialize the internal fields of the entities.
> This bug affects, for example, Nutch, which loads only some fields in it's 
> phases, serializes entities (from Map to Reduce), and when deserializes finds 
> all fields as "dirty", independently of what fields were modified in the Map, 
> and overwrite all data in datastore (deleting much things: downloaded 
> content, parsed content, etc).
> This effect can be seen in 
> {{TestPersistentSerialization#testSerderEmployeeTwoFields}}, when debuging in 
> {{TestIOUtils#testSerializeDeserialize}}. Proper breakpoints an inspections 
> shows that, entities are "equal" when it's fields are equal. This is fine as 
> "equal" definition, but another test must be added to check that 
> serialization an deserialization keeps the dirty state.

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