3.2.4: 2013-12-06

net.sf.basedb.util.overview
Class Validator

java.lang.Object
  extended by net.sf.basedb.util.overview.Validator
All Implemented Interfaces:
Action, ValidationRuleAction

public class Validator
extends Object
implements ValidationRuleAction

Placeholder for a validation rule. An object instance contains a name and description of the validation and a default severity level.

The actual validation takes place in the overview generating code. See implementations of NodeValidator interface.

Version:
2.2
Author:
Nicklas
Last modified
$Date: 2012-09-03 15:25:00 +0200 (Mon, 03 Sep 2012) $

Field Summary
static Validator ANNOTATION_INHERIT_FROM_DENIEDPARENT
          Validator rule that checks if the logged in user has access to the parent item of an inherited annotation value.
static Validator ANNOTATION_INHERIT_FROM_NONPARENT
          Validator rule that checks if an inherited annotation value is inherited from a parent item.
static Validator ANNOTATION_INHERIT_MULTIPLE
          Validator rule that checks if two or more inherited annotations have the same annotation type.
static Validator ANNOTATION_INVALID_ITEM
          Validator rule that checks if an annotation is not valid for the current item type.
static Validator ANNOTATION_INVALID_VALUE
          Validator rule that checks if an annotation value is invalid according to annotation type specification.
static Validator ANNOTATION_IS_PARAMETER
          Validator rule that checks if an annotation is a protocol parameter.
static Validator ANNOTATION_TOO_MANY_VALUES
          Validator rule that checks if an annotation have more values than what the 'multiplicity' setting for the annotation type allow.
static Validator CIRCULAR_REFERENCE
          Validator rule that checks for circular references among pooled items.
static Validator DATAFILE_INVALID
          Validator rule that checks if a data file is valid.
static Validator DATAFILE_INVALID_ITEM
          Validator rule that checks if a data file can be used on the current item type.
static Validator DATAFILE_NOTPLATFORM
          Validator rule that checks if a file is registered with a platform/item subtype or not.
static Validator DATAFILE_NOTVALIDATED
          Validator rule that checks if a data file has been validated or not.
static Validator DATAFILE_TOOMANYFILES
          Validator rule that checks if there are more than one file of a file type that doesn't allow multiple files.
private  Severity defaultSeverity
           
static Validator DENIED_ANNOTATIONTYPE
          Validator rule that checks for denied access to an annotation type.
static Validator DENIED_ANYTOANY
          Validator rule that checks for denied access the referenced item in an any-to-any link.
static Validator DENIED_ARRAYBATCH
          Validator rule that checks for denied access to an array batch.
static Validator DENIED_ARRAYDESIGN
          Validator rule that checks for denied access to an array design.
static Validator DENIED_ARRAYSLIDE
          Validator rule that checks for denied access to array slides.
static Validator DENIED_BIOPLATE
          Validator rule that checks for denied access to a bioplate.
static Validator DENIED_BIOSOURCE
          Validator rule that checks for denied access to biosource.
static Validator DENIED_DATAFILETYPE
          Validator rule that checks for denied access to data file types.
static Validator DENIED_DERIVEDBIOASSAY
          Validator rule that checks for denied access to derived bioassay.
static Validator DENIED_EXTRACT
          Validator rule that checks for denied access to extracts.
static Validator DENIED_FILE
          Validator rule that checks for denied access to (data) files.
static Validator DENIED_HARDWARE
          Validator rule that checks for denied access to hardware.
static Validator DENIED_PHYSICALBIOASSAY
          Validator rule that checks for denied access to physical bioassay.
static Validator DENIED_PLATFORM
          Validator rule that checks for denied access to platform.
static Validator DENIED_PROTOCOL
          Validator rule that checks for denied access to protocols.
static Validator DENIED_SAMPLE
          Validator rule that checks for denied access to samples.
static Validator DENIED_SOFTWARE
          Validator rule that checks for denied access to software.
static Validator DENIED_TAG
          Validator rule that checks for denied access to tags.
private  String description
           
static Validator DIFFERENT_TAG
          Validator rule that checks if the parent to a tagged extract has a different tag.
private  String failureSummary
           
private  String id
           
static Validator INCORRECT_BIOASSAY_POSITION
          Validator rule that checks if the position of an extract on a physical bioassay is between 1 and the size of the bioassay.
static Validator INCORRECT_BIOMATERIAL_TYPE
          Validator that checks if the biomaterial on a bioplate is of the correct item type.
static Validator INCORRECT_BIOSOURCE_TYPE
          Validator that checks if the parent biosource of a sample has the expected subtype.
static Validator INCORRECT_DERIVEDBIOASSAY_TYPE
          Validator that checks if a derived bioassay has the expected subtype.
static Validator INCORRECT_EXTRACT_TYPE
          Validator that checks if the parent extract of a extract/bioassay has the expected subtype.
static Validator INCORRECT_HARDWARETYPE
          Validator rule that checks if the hardware attached to an item has a correct hardware type.
static Validator INCORRECT_PHYSICALBIOASSAY_TYPE
          Validator that checks if a physical bioassay has the expected subtype.
static Validator INCORRECT_PROTOCOLTYPE
          Validator rule that checks if the protocol attached to an item has a correct protocol type.
static Validator INCORRECT_SAMPLE_TYPE
          Validator that checks if the parent sample of a sample/extract has the expected subtype.
static Validator INCORRECT_SOFTWARETYPE
          Validator rule that checks if the software attached to an item has a correct software type.
static Validator INCORRECT_TAGTYPE
          Validator rule that checks if the tag attached to an extract has a correct subtype.
static Validator MISSING_ANYTOANY
          Validator rule that checks for a missing reference in an any-to-any link.
static Validator MISSING_ARRAYBATCH
          Validator rule that checks for missing array batch.
static Validator MISSING_ARRAYDESIGN
          Validator rule that checks for missing array design.
static Validator MISSING_ARRAYSLIDE
          Validator rule that checks for missing array slide.
static Validator MISSING_BIOPLATE
          Validator rule that checks for missing bioplate location.
static Validator MISSING_BIOSOURCE
          Validator rule that checks for missing biosource.
static Validator MISSING_DATAFILE
          Validator rule that checks if all files required by the platform are present or not.
static Validator MISSING_DERIVEDBIOASSAY
          Validator rule that checks for missing parent derived bioassay.
static Validator MISSING_EXTRACT
          Validator rule that checks for missing extract.
static Validator MISSING_FACTORVALUE
          Validator rule that checks for missing experimental factor value.
static Validator MISSING_HARDWARE
          Validator rule that checks for missing hardware.
static Validator MISSING_MIAME_ANNOTATION
          Validator rule that checks for missing "Required for MIAME" annotation.
static Validator MISSING_PARAMETER
          Validator rule that checks for missing protocol parameter values.
static Validator MISSING_PHYSICALBIOASSAY
          Validator rule that checks for missing physical bioassay.
static Validator MISSING_PROTOCOL
          Validator rule that checks for missing protocols.
static Validator MISSING_SAMPLE
          Validator rule that checks for missing sample.
static Validator MISSING_SOFTWARE
          Validator rule that checks for missing software.
static Validator MISSING_TAG
          Validator rule that checks for missing tag.
static Validator MULTIPLE_ARRAYDESIGNS
          Validator rule that checks if all raw bioassays in an experiment uses the same array design.
static Validator NONDEFAULT_ARRAYDESIGN
          Validator rule that checks if an item uses a different array design than specified by the project default.
static Validator NONDEFAULT_HARDWARE
          Validator rule that checks if an item uses a different hardware than specified by the project default.
static Validator NONDEFAULT_PLATFORM
          Validator rule that checks if an item uses a different platform / variant than specified by the project default.
static Validator NONDEFAULT_PROTOCOL
          Validator rule that checks if an item uses a different protocol than specified by the project default.
static Validator NONDEFAULT_RAWDATATYPE
          Validator rule that checks if an item uses a different raw data type than specified by the project default.
static Validator NONDEFAULT_SOFTWARE
          Validator rule that checks if an item uses a different software than specified by the project default.
static Validator NONMATCHING_SPOTCOUNT
          Validator rule that checks if the number of raw data spots are the same as the number of features (given a certain threshold).
static Validator NONMATHCING_ARRAYDESIGN
          Validator rule that checks if the array design for a raw bioassay matches the array design of the associated physical bioassay.
static Validator NONUNIQUE_NAME_FOR_TYPE
          Validator rule that checks if two items of the same type has the same name.
static Validator NONUNIQUE_NAME_GLOBAL
          Validator rule that checks if two items of different type has the same name.
static Validator NONUNIQUE_TAG
          Validator rule that checks if a physical bioassay has more than one tagged extract with the same tag and position.
static Validator PARENT_EXTRACT_MISMATCH
          Validator rule that checks if a child a raw- or derived- bioassay has a different extract than the parent bioassay.
static Validator TAGGED_PARENT
          Validator rule that checks if the parent to a non-tagged extract has a tag.
private  String title
           
 
Constructor Summary
Validator(String id, String title, String description, String failureSummary, Severity defaultSeverity)
          Create a new validator.
 
Method Summary
 Severity getDefaultSeverity()
          Get the default severity level.
 String getDescription()
          Get a lengthier description of the validation that takes place
 String getFailureSummary()
          Get a short summary that is displayed when the validation fails
 String getId()
          Get the unique ID of this validator.
 String getTitle()
          Get the title of this validator.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

MISSING_PROTOCOL

public static final Validator MISSING_PROTOCOL
Validator rule that checks for missing protocols. Default severity level is WARNING.


DENIED_PROTOCOL

public static final Validator DENIED_PROTOCOL
Validator rule that checks for denied access to protocols. Default severity level is WARNING.


MISSING_DERIVEDBIOASSAY

public static final Validator MISSING_DERIVEDBIOASSAY
Validator rule that checks for missing parent derived bioassay. Default severity level is WARNING.

Since:
3.0

DENIED_DERIVEDBIOASSAY

public static final Validator DENIED_DERIVEDBIOASSAY
Validator rule that checks for denied access to derived bioassay. Default severity level is WARNING.

Since:
3.0

DENIED_PLATFORM

public static final Validator DENIED_PLATFORM
Validator rule that checks for denied access to platform. Default severity level is WARNING.


DENIED_FILE

public static final Validator DENIED_FILE
Validator rule that checks for denied access to (data) files. Default severity level is WARNING.


DENIED_DATAFILETYPE

public static final Validator DENIED_DATAFILETYPE
Validator rule that checks for denied access to data file types. Default severity level is WARNING.


MISSING_SOFTWARE

public static final Validator MISSING_SOFTWARE
Validator rule that checks for missing software. Default severity level is WARNING.


DENIED_SOFTWARE

public static final Validator DENIED_SOFTWARE
Validator rule that checks for denied access to software. Default severity level is WARNING.


MISSING_HARDWARE

public static final Validator MISSING_HARDWARE
Validator rule that checks for missing hardware. Default severity level is WARNING.


DENIED_HARDWARE

public static final Validator DENIED_HARDWARE
Validator rule that checks for denied access to hardware. Default severity level is WARNING.


MISSING_PHYSICALBIOASSAY

public static final Validator MISSING_PHYSICALBIOASSAY
Validator rule that checks for missing physical bioassay. Default severity level is WARNING.

Since:
3.0

DENIED_PHYSICALBIOASSAY

public static final Validator DENIED_PHYSICALBIOASSAY
Validator rule that checks for denied access to physical bioassay. Default severity level is WARNING.

Since:
3.0

MISSING_ARRAYSLIDE

public static final Validator MISSING_ARRAYSLIDE
Validator rule that checks for missing array slide. Default severity level is WARNING.


DENIED_ARRAYSLIDE

public static final Validator DENIED_ARRAYSLIDE
Validator rule that checks for denied access to array slides. Default severity level is WARNING.


MISSING_EXTRACT

public static final Validator MISSING_EXTRACT
Validator rule that checks for missing extract. Default severity level is WARNING.


DENIED_EXTRACT

public static final Validator DENIED_EXTRACT
Validator rule that checks for denied access to extracts. Default severity level is WARNING.


MISSING_SAMPLE

public static final Validator MISSING_SAMPLE
Validator rule that checks for missing sample. Default severity level is WARNING.


DENIED_SAMPLE

public static final Validator DENIED_SAMPLE
Validator rule that checks for denied access to samples. Default severity level is WARNING.


MISSING_BIOSOURCE

public static final Validator MISSING_BIOSOURCE
Validator rule that checks for missing biosource. Default severity level is WARNING.


DENIED_BIOSOURCE

public static final Validator DENIED_BIOSOURCE
Validator rule that checks for denied access to biosource. Default severity level is WARNING.


MISSING_TAG

public static final Validator MISSING_TAG
Validator rule that checks for missing tag. Default severity level is WARNING.


DENIED_TAG

public static final Validator DENIED_TAG
Validator rule that checks for denied access to tags. Default severity level is WARNING.

Since:
3.0

MISSING_ARRAYDESIGN

public static final Validator MISSING_ARRAYDESIGN
Validator rule that checks for missing array design. Default severity level is WARNING.


DENIED_ARRAYDESIGN

public static final Validator DENIED_ARRAYDESIGN
Validator rule that checks for denied access to an array design. Default severity level is WARNING.


MISSING_ARRAYBATCH

public static final Validator MISSING_ARRAYBATCH
Validator rule that checks for missing array batch. Default severity level is WARNING.


DENIED_ARRAYBATCH

public static final Validator DENIED_ARRAYBATCH
Validator rule that checks for denied access to an array batch. Default severity level is WARNING.


MISSING_FACTORVALUE

public static final Validator MISSING_FACTORVALUE
Validator rule that checks for missing experimental factor value. Default severity level is ERROR.


MISSING_PARAMETER

public static final Validator MISSING_PARAMETER
Validator rule that checks for missing protocol parameter values. Default severity level is ERROR.


MISSING_MIAME_ANNOTATION

public static final Validator MISSING_MIAME_ANNOTATION
Validator rule that checks for missing "Required for MIAME" annotation. Default severity level is ERROR.


DENIED_ANNOTATIONTYPE

public static final Validator DENIED_ANNOTATIONTYPE
Validator rule that checks for denied access to an annotation type. Default severity level is WARNING.


MISSING_ANYTOANY

public static final Validator MISSING_ANYTOANY
Validator rule that checks for a missing reference in an any-to-any link. Eg. due to the non-relational nature an any-to-any entry may point to an item that has been deleted. Default severity level is WARNING.

Since:
2.17

DENIED_ANYTOANY

public static final Validator DENIED_ANYTOANY
Validator rule that checks for denied access the referenced item in an any-to-any link. Default severity level is WARNING.

Since:
2.17

MISSING_BIOPLATE

public static final Validator MISSING_BIOPLATE
Validator rule that checks for missing bioplate location. Default severity level is IGNORE.

Since:
3.2

DENIED_BIOPLATE

public static final Validator DENIED_BIOPLATE
Validator rule that checks for denied access to a bioplate. Default severity level is WARNING.

Since:
3.2

NONDEFAULT_PLATFORM

public static final Validator NONDEFAULT_PLATFORM
Validator rule that checks if an item uses a different platform / variant than specified by the project default. Default severity level is WARNING.


NONDEFAULT_PROTOCOL

public static final Validator NONDEFAULT_PROTOCOL
Validator rule that checks if an item uses a different protocol than specified by the project default. Default severity level is WARNING.


NONDEFAULT_HARDWARE

public static final Validator NONDEFAULT_HARDWARE
Validator rule that checks if an item uses a different hardware than specified by the project default. Default severity level is WARNING.


NONDEFAULT_SOFTWARE

public static final Validator NONDEFAULT_SOFTWARE
Validator rule that checks if an item uses a different software than specified by the project default. Default severity level is WARNING.


NONDEFAULT_ARRAYDESIGN

public static final Validator NONDEFAULT_ARRAYDESIGN
Validator rule that checks if an item uses a different array design than specified by the project default. Default severity level is WARNING.


NONDEFAULT_RAWDATATYPE

public static final Validator NONDEFAULT_RAWDATATYPE
Validator rule that checks if an item uses a different raw data type than specified by the project default. Default severity level is WARNING.


MULTIPLE_ARRAYDESIGNS

public static final Validator MULTIPLE_ARRAYDESIGNS
Validator rule that checks if all raw bioassays in an experiment uses the same array design. Default severity level is WARNING.


NONMATHCING_ARRAYDESIGN

public static final Validator NONMATHCING_ARRAYDESIGN
Validator rule that checks if the array design for a raw bioassay matches the array design of the associated physical bioassay. Default severity level is WARNING.


NONMATCHING_SPOTCOUNT

public static final Validator NONMATCHING_SPOTCOUNT
Validator rule that checks if the number of raw data spots are the same as the number of features (given a certain threshold). Default severity level is WARNING.


INCORRECT_TAGTYPE

public static final Validator INCORRECT_TAGTYPE
Validator rule that checks if the tag attached to an extract has a correct subtype. Default severity level is WARNING.

Since:
3.0

INCORRECT_PROTOCOLTYPE

public static final Validator INCORRECT_PROTOCOLTYPE
Validator rule that checks if the protocol attached to an item has a correct protocol type. Default severity level is WARNING.


INCORRECT_SOFTWARETYPE

public static final Validator INCORRECT_SOFTWARETYPE
Validator rule that checks if the software attached to an item has a correct software type. Default severity level is WARNING.


INCORRECT_HARDWARETYPE

public static final Validator INCORRECT_HARDWARETYPE
Validator rule that checks if the hardware attached to an item has a correct hardware type. Default severity level is WARNING.


INCORRECT_BIOSOURCE_TYPE

public static final Validator INCORRECT_BIOSOURCE_TYPE
Validator that checks if the parent biosource of a sample has the expected subtype. Default severity level is WARNING.

Since:
3.0

INCORRECT_SAMPLE_TYPE

public static final Validator INCORRECT_SAMPLE_TYPE
Validator that checks if the parent sample of a sample/extract has the expected subtype. Default severity level is WARNING.

Since:
3.0

INCORRECT_EXTRACT_TYPE

public static final Validator INCORRECT_EXTRACT_TYPE
Validator that checks if the parent extract of a extract/bioassay has the expected subtype. Default severity level is WARNING.

Since:
3.0

INCORRECT_BIOMATERIAL_TYPE

public static final Validator INCORRECT_BIOMATERIAL_TYPE
Validator that checks if the biomaterial on a bioplate is of the correct item type. Default severity level is ERROR.

Since:
3.2

INCORRECT_PHYSICALBIOASSAY_TYPE

public static final Validator INCORRECT_PHYSICALBIOASSAY_TYPE
Validator that checks if a physical bioassay has the expected subtype. Default severity level is WARNING.

Since:
3.0

INCORRECT_DERIVEDBIOASSAY_TYPE

public static final Validator INCORRECT_DERIVEDBIOASSAY_TYPE
Validator that checks if a derived bioassay has the expected subtype. Default severity level is WARNING.

Since:
3.0

INCORRECT_BIOASSAY_POSITION

public static final Validator INCORRECT_BIOASSAY_POSITION
Validator rule that checks if the position of an extract on a physical bioassay is between 1 and the size of the bioassay. Default severity level is WARNING.

Since:
3.0

NONUNIQUE_TAG

public static final Validator NONUNIQUE_TAG
Validator rule that checks if a physical bioassay has more than one tagged extract with the same tag and position. Default severity level is ERROR.

Since:
3.0

DIFFERENT_TAG

public static final Validator DIFFERENT_TAG
Validator rule that checks if the parent to a tagged extract has a different tag. Default severity level is WARNING.

Since:
3.0

TAGGED_PARENT

public static final Validator TAGGED_PARENT
Validator rule that checks if the parent to a non-tagged extract has a tag. Default severity level is WARNING.

Since:
3.0

PARENT_EXTRACT_MISMATCH

public static final Validator PARENT_EXTRACT_MISMATCH
Validator rule that checks if a child a raw- or derived- bioassay has a different extract than the parent bioassay.

Since:
3.0

NONUNIQUE_NAME_FOR_TYPE

public static final Validator NONUNIQUE_NAME_FOR_TYPE
Validator rule that checks if two items of the same type has the same name. Default severity level is ERROR.


NONUNIQUE_NAME_GLOBAL

public static final Validator NONUNIQUE_NAME_GLOBAL
Validator rule that checks if two items of different type has the same name. Default severity level is IGNORE.


CIRCULAR_REFERENCE

public static final Validator CIRCULAR_REFERENCE
Validator rule that checks for circular references among pooled items. Default severity level is ERROR.


ANNOTATION_IS_PARAMETER

public static final Validator ANNOTATION_IS_PARAMETER
Validator rule that checks if an annotation is a protocol parameter. Default severity level is WARNING.


ANNOTATION_INVALID_ITEM

public static final Validator ANNOTATION_INVALID_ITEM
Validator rule that checks if an annotation is not valid for the current item type. Default severity level is WARNING.


ANNOTATION_INVALID_VALUE

public static final Validator ANNOTATION_INVALID_VALUE
Validator rule that checks if an annotation value is invalid according to annotation type specification. Default severity level is ERROR.


ANNOTATION_TOO_MANY_VALUES

public static final Validator ANNOTATION_TOO_MANY_VALUES
Validator rule that checks if an annotation have more values than what the 'multiplicity' setting for the annotation type allow. Default severity level is WANRING.

Since:
3.2

ANNOTATION_INHERIT_FROM_NONPARENT

public static final Validator ANNOTATION_INHERIT_FROM_NONPARENT
Validator rule that checks if an inherited annotation value is inherited from a parent item. Default severity level is ERROR.


ANNOTATION_INHERIT_FROM_DENIEDPARENT

public static final Validator ANNOTATION_INHERIT_FROM_DENIEDPARENT
Validator rule that checks if the logged in user has access to the parent item of an inherited annotation value. Default severity level is WARNING.

Since:
2.10

ANNOTATION_INHERIT_MULTIPLE

public static final Validator ANNOTATION_INHERIT_MULTIPLE
Validator rule that checks if two or more inherited annotations have the same annotation type. Default severity level is ERROR.


DATAFILE_INVALID_ITEM

public static final Validator DATAFILE_INVALID_ITEM
Validator rule that checks if a data file can be used on the current item type. Default severity level is WARNING.


DATAFILE_NOTVALIDATED

public static final Validator DATAFILE_NOTVALIDATED
Validator rule that checks if a data file has been validated or not. Default severity level is WARNING, but this rule is not checked if the data file type doesn't have a validator.


DATAFILE_INVALID

public static final Validator DATAFILE_INVALID
Validator rule that checks if a data file is valid. Default severity level is ERROR, but this rule is not checked if the data file hasn't been validated.


MISSING_DATAFILE

public static final Validator MISSING_DATAFILE
Validator rule that checks if all files required by the platform are present or not. Default severity level is ERROR.


DATAFILE_NOTPLATFORM

public static final Validator DATAFILE_NOTPLATFORM
Validator rule that checks if a file is registered with a platform/item subtype or not. Default severity level is WARNING.


DATAFILE_TOOMANYFILES

public static final Validator DATAFILE_TOOMANYFILES
Validator rule that checks if there are more than one file of a file type that doesn't allow multiple files. Default severity level is WARNING.

Since:
3.0

id

private String id

title

private String title

description

private String description

failureSummary

private String failureSummary

defaultSeverity

private Severity defaultSeverity
Constructor Detail

Validator

public Validator(String id,
                 String title,
                 String description,
                 String failureSummary,
                 Severity defaultSeverity)
Create a new validator.

Parameters:
id - A unique ID among all validators
title - The title for the validation rule
description - A lengthier description of the validation that takes place
failureSummary - A short summary that is displayed when the validation fails
defaultSeverity - The default severity level of the validation
Method Detail

getId

public String getId()
Get the unique ID of this validator.

Specified by:
getId in interface ValidationRuleAction

getTitle

public String getTitle()
Get the title of this validator.

Specified by:
getTitle in interface ValidationRuleAction

getDescription

public String getDescription()
Get a lengthier description of the validation that takes place

Specified by:
getDescription in interface ValidationRuleAction

getFailureSummary

public String getFailureSummary()
Get a short summary that is displayed when the validation fails

Specified by:
getFailureSummary in interface ValidationRuleAction

getDefaultSeverity

public Severity getDefaultSeverity()
Get the default severity level.

Specified by:
getDefaultSeverity in interface ValidationRuleAction

3.2.4: 2013-12-06