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java.lang.Objectnet.sf.basedb.util.fileset.SingleFileValidationAction
net.sf.basedb.util.affymetrix.CelValidationAction
public class CelValidationAction
Action for validation of CEL files in a file set. The
CEL file must be connected with a RawBioAssay
.
The raw bioassay should have an ArrayDesign
that
has a CDF file matching the chip type.
This class is just a wrapper for CelValidator
so
that we can hook the validation into the extensions system.
Field Summary | |
---|---|
private DbControl |
dc
|
private RawBioAssay |
rba
|
private CelValidator |
validator
|
Constructor Summary | |
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CelValidationAction(DbControl dc,
RawBioAssay rba)
Create a new action. |
Method Summary | |
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void |
resetMetadata()
Reset all metadata that this class normally can set. |
void |
validateAndExtractMetadata()
Validate and extract metadata from the file(s) that has been added to this validator. |
Methods inherited from class net.sf.basedb.util.fileset.SingleFileValidationAction |
---|
acceptFile, getAcceptedFile |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private final DbControl dc
private final RawBioAssay rba
private final CelValidator validator
Constructor Detail |
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public CelValidationAction(DbControl dc, RawBioAssay rba)
dc
- An open DbControlrba
- The raw bioassay the CEL file is connected withMethod Detail |
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public void validateAndExtractMetadata() throws InvalidDataException, InvalidRelationException
ValidationAction
ValidationAction.acceptFile(FileSetMember)
method
returns Accept.VALIDATE_IMMEDIATELY
this method is called
and the validator should work on the last accepted file.
This method is also called after all files has been processed if at
least one file returned Accept.VALIDATE_LATER
.
This method is recommended to throw an InvalidDataException
or a
subclass if the file is not a valid file. PermissionDeniedException
:s
are ignored by the core and will not change the validation status. An
exception of type InvalidRelationException
can be thrown if the
file itself is valid, but a related file that it depends on is not. The
core will still mark the file as invalid and store the error message,
but extracted metadata will not be reset.
InvalidDataException
- If the validator detects an invalid
file
InvalidRelationException
- If the validator detects that the
file is valid but another file that it depends on is not, metadata
extract will still happenpublic void resetMetadata()
ValidationAction
|
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