Opened 11 years ago

Closed 11 years ago

#915 closed defect (fixed)

NullPointerException when a raw data type is missing

Reported by: nicklas Owned by: nicklas
Priority: major Milestone: BASE 2.6
Component: core Version:
Keywords: Cc:

Description (last modified by nicklas)

If a raw data type is removed from the raw-data-types.xml file and there are raw bioassays in the database that uses the removed raw data type, the call to RawBioassay?.getRawDataType() will return null. This causes a lot of trouble for many parts of the code since null is not an allowed return value. I think the Experiment.getRawDataType() may be affected by the same problem.

Since the configuration is in an external file there are no database constraints that we can lean on to make sure that used raw data types are never deleted. Maybe we can have a "dummy" raw data type so we don't have to return null.

Example stacktrace:

   at org.apache.jsp.views.rawbioassays.list_005frawbioassays_jsp._jspService(
   at org.apache.jasper.runtime.HttpJspBase.service(

Line 1295 in list_rawbioassays.jsp is:


Change History (3)

comment:1 Changed 11 years ago by nicklas

  • Description modified (diff)

comment:2 Changed 11 years ago by nicklas

  • Owner changed from everyone to nicklas
  • Status changed from new to assigned

Hmmm.... I have checked the code and the RawDataType? is used in a LOT of places. I don't think returning a "dummy" object would be of any help. It would just delay the exception until later and would probably confuse things even more. Instead, I think it is better to modify the RawDataTypes?.getRawDataType() method to throw an exception if the raw data type is missing. This introduces a backwards compatibility problem for client code that have actually followed the documentation and checked if the return value is null or not.

Hmmm... maybe it is better to instead add a RawDataTypes?.getSafeRawDataType() that throws an exception. It will not affect other client code, and we can easily change our own code to use the new method instead.

comment:3 Changed 11 years ago by nicklas

  • Resolution set to fixed
  • Status changed from assigned to closed

(In [4124]) Fixes #915: NullPointerException? when a raw data type is missing

Use RawDataTypes?.getSafeRawDataType() instead, which throws an exception immediately.

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